I hate Aerodactyl
It took me ~4 tries and ~10 Revives and ~15 Super/Hyper/Max Potions to do it, trust me, it was harder than a Ninetales in rainy weather, because tanking too much Ancient Powers makes your whole team faint.
And probably the worst part was, I got there when it was partly cloudy, but right before I finished my final try, the weather changed to Sunny! I felt like I was battling a partly cloudy Aerodactyl, but catching a Sunny one. And here is yet another frustrating thing: 10 meters away (aka the other side of the gym) was Windy. WTH were you serious?
I went for a raid because I wanted a weather boosted Aerodactyl, but ended up with a loss of several revives/potions and a normal (at least it got a decent moveset SW/IH and good IVs lol) Aerodactyl.
Yes, I didn't use my Kyogre. Why? Because I didn't think of it at that time, I even threw in Dragonite and Snorlax in because I thought I had run out of options.
Answers
Ancient Power is super easy to dodge. I've done Aerodactyl with all Jolteon and all Vaporeon teams so far and yes, it can be punishing with a glassy team, like all Jolteons. There's a bunch of tanky counters viable at level 30 including Raikou, Kyogre, Vaporeon, Metagross, Aggron, IT/SE Tyranitar, Swampert, pretty much any 2 of them after 4 glassier attackers should ensure you last the raid.
Whether the loss of DPS is important depends. Aerodactyl doesn't have high defense so you can dodge all charge moves with any halfway decent counter, like level 30 Jolteon. Does require a bit of prep to know this of course. But I would always prioritize staying alive because the DPS loss from rejoining is absolutely massive and generally means failure. Then if you time out you can start adjusting your team and strategy to get more DPS.
No, It doesn't seem to be insanely hard, 2 Level 30 or above Kyogres should be able to take it down. Even if you don't have Kyogre, If it does not have Ancient Power you can use Gyarados, And you can always use Vaporeons, Aggrons, Tyranitars, Metagross and Scizors as counters if you missed the whole kyogre season. It's nothing compared to Claydol and Alakazam which i don't want to solo at all. If i would compare it with another T3 it's around Omastar difficulty.