Personally, I started with rejuvenation, mainly because that was the game I found first (yeah, I actually managed to find rejuvenation on the reborn forums before I found reborn and realized later I was looking at the site referring to the game my boyfriend played atm),
Anyways, there's no real advice to give I believe. If you've got a hell of a lot of time, go for reborn - because you will need that and it won't disappoint you.
If you've got a lot of time but not actually a real lot, go for rejuvenation - because it's just eight badges yet and it won't disappoint you either.
In Reborn most secrets are found by the community, there are a whole bunch of nice videos on youtube explaining how to get those event 'mons. You don't have that in rejuvenation just yet (and I don't know how many secrets there actually are - if any - that get close to the ridiculousnes of some of those in reborn *yeah, I'm looking at you, beldum*).
Both storys are awesome, both games get you hooked up. I also like the sprites and the general look of rejuvenation a little more, but seriously, you won't care for long.
Anyhow: Just download both - there's always the chance some pokemon get axed in the next version ;P