Rysabi
Oh jeez, I've been playing Pokemon since Red/Blue were brand new. I own nearly every Pokemon game released, I also have some physical copies of fanmade rom-hacks.
My favourite legit game would be Emerald, I think they got a lot of things right with that game. I spent tons of hours on it. Lots of memorable experiences with it.
My favourite rom-hack would be Liquid Crystal. I dig the storyline and there is just so much to do plus there is a bunch more Pokemon available than the legit Crystal version that was released from Nintendo.
Emerald was a good game from the Hoenn region, but I found that the Omega Ruby and Alpha Sapphire versions of the Hoenn region did a much better job. I loved the fact that you could fly across the sky on a Latios or a Latias. I liked how you could try and find legendaries, but not always catch them.
Another Pokemon game that I liked was Pokemon Sword. I liked the camping feature they added. Granted they could have added more into it like mega evolutions, but for what they did do I am impressed. Plus, their Pokejobs feature was a good thing too.