I have two games: Sapphire and LeafGreen. My LeafGreen game is complete, so I have access to high levelled wild Pokemon. I recently just started Sapphire again. If I trade one of my Sapphire Pokemon to LeafGreen, level them up there a lot with the EXP Share and then trade them back to Sapphire, will they still obey me, since the Sapphire Pokemon will still have the same IDs as me?

I don't know, but I suspect not, because their happiness levels will be reset by trading, which I believe is one of the major factors in whether pokemon will obey you past the level limit; your own pokemon that are that high presumably have very high happiness, just from the process of levelling them up, but ones you trade don't. That would be my personal theory, at least; I've never tried it.

I sent my Wingull shortly after beating Roxanne to LeafGreen and levelled it up to Lv30 there. I then traded it back and it is obedient, despite me not reaching Brawly yet.

how did you trade to lg if sapphire hasnt gotten the national dex

If I recall correctly, you obtain the National Dex once you obtain a Pokemon that is not in the Hoenn Dex. You can trade even if you only have the Hoenn Dex (you will come out of the trading room with a National Dex).

Is sorta goes with what everybody else says buti pretty sure that if your pokes are a higher level than your gym badge and there is a certain percent that pok will obey you the percent will rise when the happiness rises I think

how many badges you got? if you trade-levelup high-trade back and still are at same spot in sapphire story, the pokemon will not obey you because you "got not enough skill in their eyes." you need x number of badges so you can controll up to Y lvl of pokemon.

I don't know which badge make which lvl obey... but I assume that the number of obeying Pokemon, raise with number of gyms and lvl of pokemon found in wild/ trainer battles.
Example: Roxanne's Badge may do so that Pokemon -> 20 obeys you. when Brawley's Badge do make pokemon up to lvl 30 obey you etc. If you had read when you got a gym badge...

"blablabla"... Pokemon up to lvl X will now obey you.

It'll still obey you.

Disobedience is determined by the OT and ID number, not by happiness.