Well you should run something like this for a list
3 skyla (rare candy, level ball catcher etc, running 3 is important, running 4 might be better, depends on how it works out for you)
4 N
3 juniper
3-4 cheren or bianca
2 random receiver
3 level ball (great setup card, better then playing shaymin or emolga, reduces the amount of cards in you're deck to play the cards you need, grabing a bunch of basic's in a stage deck is like putting up cannon fodder for landorus or mewtwo)
3 switch (I would go 4, but it depends, they will catcher you're engine alot even withoput attacking just to make certain that it's hard for you to bounce back or so called waste a card, so it's good to have 3 minimum)
2 super rod (lets you grab three, and helps bring back the tier system
3-4 catcher (it's great for not having to attack, even if you're running celebi it's not like flygon has alot of hp, so bringing up and stalling with bench techs or slow cards does sometimes work)
2-3 rocky helmet (there is alot of people that would say go for the giant cape, extra 20 is kind of handy, thats newb talk I hear at the league all the time, you're dealing accumulative dmg, just keep building it up regardless, you're going to take heavy hitting damage anyways so might as well use it towards you're advantage, 1 prize to they're 2 that's all you need)
4 rare candy (there's a reason I went 2 super rod and 4 rare candy with probably a 4-1-3 line of flygon)
If you like crush, put in crushing hammer and enhanced hammer, the rest is up to you
this is a skeleton, and a basis behind what probably makes the engine run the best.
Edit: I would also mention, add another mainline attacker like an EX, that would help, mewtwo, landorus, keldeo, something that uses the energy flygon uses.