It is up to personal preference, although, in my opinion, Groudon beats Kyogre in a 1 versus 1 situation most of the time. I picked Alpha Sapphire though. The difference between version won't matter in the long run, but it does change the storyline somewhat.
And for what starter you should pick is also personal preference, but I'd pick Torchic. Its final evolution is insanely strong and is also decent against your opponents Mudkip and its final evolution.