I funneled down all my raid (not rare) candy to power up my best shiny (93%) instead of my best overall (96%) just because the former is shiny.
If I was in your situation I would do the same: the difference in IVs is negligible (breakpoints ignored) and being able to save a little in resources is worth it for how useful it will end up being.
Give your Lugia opinion
I hit Lugia hard this month and over 20 raids I finally got a weather boosted Shiny with 15 attack as a reward for my efforts. I think that's the one I should invest TMs and dust into. Do you agree? These are my best Lugia options.
1) 2551 CP, 15HP, 15A, 10D (89%) (weather boosted AND SHINY)
2) 2539 CP, 13HP, 14A, 13D (89%) (weather boosted)
3) 2538 CP, 15HP, 13A, 13D (91%) (weather boosted)
4) 2042 CP, 14HP, 15A, 12D (91%)
5) 2035 CP 14HP, 14A, 13D (91%)
The only knock on #1 is the relatively low defense. Does that even matter for Lugia? Do the weather boost and Shiny out weigh and loss on the Defense stat?
Which would you power up?
Answers
Having high defence doesn't mean defensive breakpoints don't exist for that Pokemon. If anything defensive breakpoints have more effect on high defence because Pokemon with high defence will reduce damage to smaller values which makes -1 damage have a higher relative impact.
For example reducing damage from 4 to 3 is a 25% reduction in damage, while reducing damage from 10 to 9 is only a 10% reduction.
Plus 15 defence is a requirement if you're trying to 1v1 Machamp in cloudy weather since Counter does 3 damage rather than 4 vs a 15 def level 40 Lugia.
I'd still power the shiny one because it has 15 attack, none of the other Lugias have both 15 attack and defence, plus it's weather boosted which will save a few candies.
What outweighs the low defense is that Lugia has an obscene defense already. 15 stamina and 15 attack make it the best choice, never mind the highest CP.
If you want to power up two (maybe one for Machamp raids and another for gym sweeping), #3 is also quite good, although you should check the stats, if it's 15/13/15 (s/a/d) then it's a 96%. But it's hard to justify powering up two if you have a single Kyogre, Groudon, Rayquaza, Moltres, Raikou, or Mewtwo, even if they have bad IVs.