Let's face it, the fast majority of games here are Pokemon fangames. Some staying really similar to the original ones, others are mixing the gameplay completely up.
To all developers: Gameplay-wise, how much are you willing to stray from canon? Would you implement big changes to the gameplay, if you had the ability to? What are the things you'd really like to see? Are any elements of the original games that should absolutely never be edited?
To those interested in playing fangames: What are you looking for in a fangame? Again, how do you think about major edits to the gameplay?
If your making a remake, to me, EVERYTHING MUST BE HOW IT WAS!
That goes from, adding new houses, new places, getting rid of pointless events, speech, battles, characters, wild pokemon.
I get pretty picky with this stuff.
If it's random appearence in games, I'd like them to have reasons, like Oak is in the ashrloai region because a new species of pokemon was discovered. Or something like that.
I kinda feel I'm rambling or have no idea what I'm on about, but I'll continue.
But as for Non-Canon things, the only one I like; Isn't a fan game, but a ROM hack, Pokémon Dark Violet. Everything is non canon, but it's pulled off in the most legit way, it makes it seem like it is Canon, and Pokemon Red/Blue and Yellow are Non-Canon.
In my game, I'm leaving other stories and region themes well enough alone, so I don't mess up Canon to Non-canony stuff, except when the game is done, and you can enter the PWT, do you see old characters.
Part of the reason I wanted Orange Project to be basically separate from all the canon games, with a completely new Pokedex and all, was so that I could flout canon whenever it would benefit the game (not that anything much has come up). It also means I don't have to keep up with new generations as much.
I don't think I'd make any huge changes to the gameplay itself, since there's nothing about the way the games work that really bothers me (except maybe the typechart :P), and anyway I probably wouldn't be able to figure out how to program any of it.
The fun about this question is that everyone would have to specify what canon is. A remake is a remake, as Nintendork15 said. So FR/LG are not so canon in this way that stuff from later generation was added, first of all two types which weren't in RBGY.
Next, I don't see it is uncanon to put "other canons" like the anime or one of the mangas (Adventures for example) into a game, as long as the player sprites are changed acordingly.
If someone comes up with a realistic scenario, that shouldn't be a problem, too. For example, to gather any girl for my Dating Sim, a world tournament is being held. So far so good. But then the girls could have any appearance they ever had AND (of course) they are 18, so their appearance isn't matching their age at all. In addition I'm mixing up different canons (as described above), for there will be e.g. Red (the uber fan version) AND Ash, so that's a little bit confusing.
As for the DAYW-Version (Do Anything You Want, yay I just came up with a title!), it will be the (original but improved) setting of FR/LG. But more "our reality"-canon, so basically anything could happen and "reality bugs" of the game (e.g. why would you only find certain pokemon in either FR or LG? Reality crack? Or e.g. all people let you in their houses.) get fixed.
For most fandoms, it is not right, but in Pokemon "canon" is actually a matter of perspective. But of course you can still be uncanon in every way xD