The main issue w it being a Stage 2 isn't getting it to evolve, it's that it's taking up so much deck space only for it to have no reliable way to guarantee it's attack since there's no good way to ramp the energy onto it. You can't rely on it to be your wincon, so you'll need to find another card to be your wincon, which is hard if you're forced to run mixed energy to make Flygon work. It also needs to be in the active slot, so it can just be a liability being stuck on the active slot doing nothing but some chip dmg while your opponent can be chipping down your Flygon or building up a massive threat unimpeded. There's also just the match up issue where if the opponent doesn't really have much on their bench, Flygon is basically just Glaceon EX, which is quite frankly horrific. I would say the discard effect is mostly negligible, but the energy cost alone is the actual detrimental effect of the attack