I think both would of most likely suffered, but Batista would of been an afterthought if he had not been in Evolution.
Lets look at the facts, it was really HHH and Ric Flair that brought out Batista's personality as you could clearly tell that the longer he was in evolution, the better he was getting on a week to week basis (for the first year he was in Evolution he was more of a background player (although injuries certainly played a part in that)). I think through HHH and Flairs efforts Batista was able to learn more about the business, what it was about, how to get over with fans, put on a decent match, all of these things were instilled into Batista by flair and hunter (don't believe me, watch Batista before he was in Evolution, then watch him literally grow through his time in Evolution and now look at where he is), Batista gets a HUGE nod for listening and being able to pick up all this knowledge he was given, and learned how to use all this knowledge to his advantage, but if HHH and Flair didn't give it to him in the first place, Batista would have never gotten past the Vladimir Kozlov stage, a big guy who beats on jobbers but fails miserably when they are actually put in a program or are given a push.
Cena on the other hand didn't need Flair and HHH to get over, and I don't think he would of done better (probably closer to what hes doing now) or gotten over more being in Evolution, if anything it would of halted his growth. Obviously you can learn volumes worth of stuff from HHH and Flair, but Cena already had the X factor coming into the WWE (he was over in his first match against Angle for Christ sake, how many people can say they were actually OVER in their first televised match, I always knew Cena was a big star waiting to happen), and most of all he just didn't fit in with Evolution. He got over much better basically being himself (and apparently he is nothing more than a new age Mark-E-Mark) with the volume turned up. What really got Cena over with the fans was his Mark-E-Mark rapper gimmick and mic work using that gimmick, if he was in Evolution, this gimmick wouldn't of happened in 2003 (as he would of been doing basically Batista's gimmick) and I just don't think he would have gotten nearly as over as he did being a rapper, the Batista gimmick doesn't really fit well on John Cena.
All in all things worked out for the best the way they did, Cena didn't need Evolution, Batista did, both guys got insanely over with the fans and everyones a winner.