I think my overall favorite here would be Sapphire/Ruby/Emerald and then Emerald in particular.
Of course I give the "original" it's fair share of praise, being the one who introduced us to the wonderful world but I can surely say that it is not the one I see as best. From what i have seen and heard, it's a pretty flawed experience and there are a lot of bugs, etc.
So yeah, I think Emerald would be my overall favorite game
OMG they used Colors when they named Red and Green,... How original Gamefreak, i am disappoint