Current way of determining best moveset flawed?

Well, the first problem with this conversation for me is that I misunderstood the phrase "if you're not short on time" in your initial post as how much free time I can spend fighting gyms. Apparently, you were referring to the 99 seconds time limit for each round of gym battle.

Unfortunately, like I illustrated in my own case scenario, I will be at a distinct disadvantage if I can't take down my neighborhood gym fast enough, so even though I certainly can't speak for everyone, wasting time by conserving hp and items is a problem for me personally.

Secondly, if you'll spare me some time, I would like to illustrate a worst case scenario by assuming that you, as a player, are in a situation where potions and revives are scarce and you're trying to take down a level 10 gym filled with 10 rival Snorlax of an average of 2000CP and 50% IV each (note: this is because in the current metagame, Snorlax has no effective counter, not even a pokemon with type advantage against it, so no matter which pokemon you choose to fight it, there won't be much of an advantage), with 6 of your strongest pokemons also at 2000CP and 50% IV each.

You'll be using your tactic of quick moves + dodging. The opponent AI will of course be using a combination of quick moves (Zen Headbutt) and charged moves (Hyper Beam) as much as it can by alternating both type of moves for all 10 Snorlax.

For reference, in my experiences, I can take down a single 2000CP Snorlax with a 2700 Dragonite in 35 seconds with minimum dodging and end with 30% hp left.

For this scenario, I'm going to assume that by employing your tactic, you can finish each round in 90 seconds with 40% hp left. From what I know, no matter how well you can dodge, you will still take at least 25% of the total damage that each hyper beam was supposed to inflict. And due to the amount of time spend fighting a single Snorlax, it is reasonable to believe that each Snorlax will be able to use Hyper Beam at least twice in each round.

To simplify the equation, we'll asuume it's a 25% hp loss from dodging a hyper beam, considering the fact that you are using pokemons of equal CP as your opponents. Therefore, (25%+25% from Hyper Beam) + (10% from Zen Headbutt)= 60% of hp lost each round for your pokemon.

By fighting to the death, you should be able to clear all 10 Snorlax in the gym with only 1 pokemon left, as long as you can dodge and attack perfectly. It will take you 900 seconds. You will bring down the gym prestige by 6500 (500x10 for each defeated Pokémon + 1500 for full clear bonus) and gain 1050 XP (100x10 for each defeated Pokémon + 50 for full clear bonus).

However, according to you in your first post, if you were to alternate between quick moves and charged moves + dodging only for opponent's charged moves, you will take less than half the time than you normally need for your quick moves + dodging tactic. Let's assume that you are now employing the former tactic and run through the same scenario with most of the same conditions again, though we will have to assume that all 6 of your pokemons also have Hyper Beam as their charged moves.

Simply put, this time, you will take far more damage and far less time per round, but be forced to finish the fight without clearing all 10 Snorlax. Fortunately, I am experienced with this tactic, and I can guarantee you that in this situation, because of the speed at which each round will end, each Snorlax will only be able to use 1 Hyper Beam, which you will dodge (because that's is the most logical thing to do).

By fighting to the death, you will take 45 seconds for each round, which is half the time it takes for your quick moves + dodge tactic. I can tell you that you'll be able to beat each Snorlax with just 2 Hyper Beam in addition to the quick moves, as long as you use it as soon as the charged gauge is full. You should be able to end each round with only 25% health left (25% total damage from Snorlax's Hyper Beam with dodging + 50% total damage from Snorlax's Zen Headbutt with no dodging), but you'll enter the next round with a fully charged gauge, which you'll be able to unleash as soon as the next round starts.

To simplify things, you are trading 75% hp to beat each Snorlax, and you'll be able to only beat 8 Snorlax at most before you are unable to battle. It will take you 360 seconds (45 seconds x 8 Snorlax). You will bring down the gym prestige by 4000 (500x8 for each defeated Pokémon) and gain 800 XP (100x8 for each defeated Pokémon).

However, this is only in theory. Frankly, there are also many other variables when it comes to optimizing resources, whether it be time or potions.

For example, with quick moves + constant dodging, you will spend 900 seconds to bring down 6500 prestige, while with the charged moves + quick moves + 1 dodge per round tactic, you will spend 360 seconds to bring down 4000 prestige. You can easily hit the gym twice with the 2nd tactic to bring the gym down by 8000 prestige and spend only 720 seconds in battle, in total.

However, you will need to revive and heal all 6 pokemons in between the two battle attempts. That's a minimum of 12 super potions (note: even a 100% IV Snorlax with 2001 CP will only have 212 max hp, therefore if you use revive on all 6 pokemon, chances are you only need to use 2 hyper potion at most to get each to full/near full hp) and 5 revives (note: there is no reason not to flee from battle after beating the 8th Snorlax, so you will be able to save 1 revive but spend 2 more hyper potion), not to mention about 30 seconds spent in the item section healing your pokemon and another 10 seconds to start the 2nd round of gym battles.

So to compare the two tactics,

Tactic 1: quick move + constant dodge
Time: 900 seconds
Items Spent: none
Prestige: -6500
XP: 1050

Tactic 2: quick move + charged move + 1 dodge
Battle Attempt 1
Time: 760 seconds
Items spent: 12 hyper potion + 6 revive or 14 hyper potion + 5 revive
Prestige: -8000
XP: 1600

Of course, at the end of the day, you will definitely have to use whatever potions and revives you possess to heal the 6 injured pokemon you've used. But since that's common for both tactic, I've left that out. As you can see, depending on what the player values most, each tactic can be just as suitable and applicable as the other. It depends on how you define a "successful strategy".

Also this is assuming that it's a level 10 gym. If it was just a level 8 gym:

Tactic 1: quick move + constant dodge
Time: 720 seconds (90 seconds x 8 Snorlax)
Items Spent: none
Prestige: -5500 prestige (500x8 for each defeated Pokémon + 1500 for full clear bonus)
XP: 850 XP (100x8 for each defeated Pokémon + 50 for full clear bonus)

Tactic 2: quick move + charged move + 1 dodge

Battle Attempt 1
Time: 360 seconds (45 seconds x 8 Snorlax)
Items spent: none
Prestige: -5500 (500x8 for each defeated Pokémon + 1500 for full clear bonus)
XP: 850 XP (100x8 for each defeated Pokémon + 50 for full clear bonus)

Note: after the first battle attempt, the gym level will drop by 1 level if the amount of gym prestige drops below the threshold, and become a level 7 gym, and so the number of Snorlax in the gym will also drop by 1 accordingly. If this did not happen, attempt two will yield the same result as attempt 1 in terms of prestige and xp. We'll assume it's now a level 7 gym for this scenario.

Tactic 2: quick move + charged move + 1 dodge
Battle Attempt 2
Time: 355 seconds (45 seconds x 7 Snorlax + 40 seconds on healing)
Items spent: 12 hyper potion + 6 revive or 14 hyper potion + 5 revive (maximum number in worst case scenario)
Prestige: -5000 (500x7 for each defeated Pokémon + 1500 for full clear bonus)
XP: 750 XP (100x7 for each defeated Pokémon + 50 for full clear bonus)

Tactic 2 total:
Time: 715 seconds
Items spent: 12 hyper potion + 6 revive or 14 hyper potion + 5 revive (maximum number in worst case scenario)
Prestige: -10500
XP: 1600

As you can see, in pretty much the same time it takes you to use tactic 1 once, you can use tactic 2 twice and inflict more prestige and earn more xp at the expense of using more items.

I know I've taken a lot of liberties at the calculation and assumptions, but the reasoning is still the same; in this case, you'll either spend more time and less items or you'll spend less time and more items. Even if someone's tactic is to only beat the first pokemon of each gym before fleeing, and thereby dropping the prestige by only 500 every 2 minutes, saving all his revives while using up a lot of potions, that player will still be trading something he might not value (time and potions) for something else he probably values more (revives).

No matter how you look at it, the same lesson as the level 10 gym battle scenario is applicable here; It depends on how you define a "successful strategy". If time is an affordable commodity to you, nobody can say that you're wrong.

To tie this back into the original question of whether the moveset ranking system is flawed because it doesn't take damage taken into account, let me summarise and clarify my original reply.

The tl;dr version is: Everyone knows it's flawed. The moveset ranking is only applicable if you remove a bunch of variables like type advantages and dodges from the equation.

The moveset list/ranking was created to allow the players to determine the best pokemon to keep as either an attacker or a defender by judging on their movesets. That's literally it's only purpose.

And as you can see, the moveset ranking for both Attacker and Defender are completely different, due to the behavior of the gym AI. In fact, in one of the excel sheet I've linked previously, the author actually does acknowledge under the column of "no weave damage" that for some movesets, continuously spamming the quick moves only, while ignoring charged moves will yield a better dps.

Dodging isn't included as a criteria for ranking pokemons strengths, as seen under the column "Duel Ability", which is defined as "a reasonable measure if you don't often/ever dodge, as then you can only attack for as long as you can stay positive on HP."

But it's not like you can switch your moveset after you've caught or evolved your pokemon, and players have to choose which of their numerous pokemons of the same species they would power up, based on their IVs and movesets. Sometimes, I would power up a low CP, high IVs pokemon with a good moveset and spend a great amount of stardusts and candies. In principle, this is exactly the same as the gym battle tactics scenarios that we've discussed. I valued the IVs and moveset more than the stardusts and candies because of their unpredictability, just as you did for potions and revives spent vs time spent in gym battles. For me, I have so much potions I needed to toss them to make space. If the situation calls for me to use more potions and save more time, I would say, why not? But my situation is unique only to me, and isn't applicable to you, right?

So, unfortunately, as logical as your idea is, when I'm fighting a level 7 gym every day for 15 minutes straight alone, dodging every single attack is just too much for my concentration. That's why I always prepare my team 10 minutes before I hit the gym, and choose all my pokemons with type advantages and the proper movesets based on the opponent pokemons. Your logic is sound in theory, but not really practical for me, where all the gyms here are right in the middle of the 3 different apartment blocks.