easy retcon: shiny colors. they've done it before - look at FRLG's shiny golbat and compare it to other versions. also gender differences in sprites.
aesthetic changes would probably be the easiest to do, as GF doesn't even need to mention them. these changes don't effect gameplay nor compatibility with other versions.
(moves/abilities also fall under "easy" retcon, as GF often alters movesets even between games.)
more difficult retcon: evolution methods. why couldn't eevee evolve with a sun stone before now? maybe in the new region, evolution stones are more powerful and effect more pokemon. i'd say breeding items also fall under this.
this kind of change needs active explaining to fit in: even though there is no direct effect on older games, players might get confused if changes aren't mentioned or explained. imagine spending the whole game wondering why your max. happiness eevee just won't evolve.
extremely difficult/improbable changes: pokemon gender and evolution lines**. these would be hardest because they would restrict transfers between games, either by preventing the transfer altogether, or by altering the pokemon upon transfer.
using the example of gardevoir prople have been discussing above: if GF made that pokemon female-only, anyone trying to transfer a male gardevoir to new games would either get a "this trade is impossible" message, or would be in for a rude surprise upon completing the transfer.
even if given a warning along the lines of "this pokemon will be altered if you transfer it", the fact that such a change would have an impact on game connectivity like this makes me believe it would be highly unlikely.
**this is different from evolution methods - after all, feebas' method changed without much fuss. changing evolution lines would be like combining luvdisc and alomomola's lines into one. split evolutions are a bit easier to explain away - like a new item being discovered, or a brand-new move learned. but taking two completely unrelated pokemon and making them one would be really difficult imo.
new typed are, in my opinion, a tricky case. on one hand: if a certain type only exists in a certain region, not having it in older regions could be explained. but changing existing pokemons' types seems harder to explain, to me. GF did it in gen II (i.e. magnemite), and again in gen V (rotom formes) without really explaining. but the first time was so early on in the franchise, and the most recent was a fairly minor alteration, i can't really predict or imagine how a new type would be introduced/explained at this point...
if you got this far: thanks for reading! and my apologies if it doesn't make much sense, this was moslty just me thinking out loud.