I got Ruby because I liked Groudon more than Kyogre and I wanted Latios since it was male. But if you have too choose between them I would just wait until Emerald is out. In case you were wondering some of the features in Emerald are :
you get rayquaza before the elite four
you get both Groundon&Kyogre after the elite four at level 70
you get sudowoodo
the battle frontier
if you get the tickets+ old sea chart you can get a combination of ho-oh,lugia,speed deoxys, and mew
you get to choose your Lati
Emerald is the only 3rd genration(R/S/E) that uses the wireless adapter
and you get Johto pokemon in the safari zone once you beat the E4