where it's even specifically stated that you should try to win with your favourites as opposed to simply what's good, and trainers that only base their teams on power are often disparaged or considered bad trainers.
tbh I interpret that as more "try things outside your comfort zone" as opposed to using the same staples all the time. There are 720 Pokemon, there is no way to balance even just the fully evolved ones so that everything is viable - even if base stats were the same, you still have to take movepools, abilities, and typing into account. Fuck, Blizzard can't balance 11 classes in WoW for shit and Riot has trouble keeping tabs on 100-something champions (miracle that LoL is as balanced as it is), what chance does Gamefreak have with so many variables they made? Better to focus on merchandising than staying true to in-game dialogue.
Your storyline Pokemon are still more than likely not going to be any good even with the IVs and training factors removed because of the lack of egg moves, probably suboptimal nature, and arbitrary distribution of Pokemon (mons that appear early-mid game are more likely to be picked than something like Noibat that first appears in Victory Road).
That being said, I'm in the precarious position that my favorite Pokemon (seen left) is banned in all Nintendo tiers and little kids cry about legendary Pokemon being "cheap" even if you use them when they're allowed so in some ways bullshit people say in-game can be fairly hypocritical :|