I would say because of the changes to the champion you should pick treeko and avoid torchic because of the type weakness to the champion.
Mudkip is a great choice as well when it oses it weakness to electric because even though it gets 4x weakness to grass there arent many strong grass pokemon/grass moves in the storyline (except rival battle to a grovyle with leaf blade).
And yes, emerald is greatly better than RS due to the frontier and more catchable poekmon without trading. ;123;