A reader posed the above question to me the other day (which you can also do so at anytime here) although it came without much more of an explanation. I assume that it was fantasy based, but I'll tackle it from both fantasy and real-world angles.
I think I'm slightly higher on Adam Eaton than most, so I'll lead with that caveat. The decision between him and Marte is interesting. It gets down to the question of what adds more to a prospect's value - ceiling, or the chances of reaching that ceiling. When it comes to roster planning, I also tend to put more stock in reliability than others. You've been forewarned.
Starling Marte has more tools in his pinkie finger (I heard a source say he's got a potential 70 small appendage) than Eaton has in his whole body, but Eaton is so much better at using what he has. Marte could be a star, but there's also a decent chance he never learns to hit that slider from right-handers that so many players never figure out. He'd be a CF on most teams but won't get a chance as long as Andrew McCutchen is still the Pirates best player. Marte had more power than Eaton too. I just don't think he will get on base much. I see a lot of .280/.335/.450 seasons in his future.
Eaton, on the other hand, should do something like .275/.370/.420 in his prime and steal bases too. If he manages to hit .300, he'll be the best leadoff hitter in baseball not named Trout.
Then there's the playing time question, which I discussed for Eaton earlier this fall. The Pirates are going to put Marte out there everyday regardless of any struggles, at least for this season and probably for the next few unless it really gets ugly for some reason. If I has to guess on Marte this season, I'd say .268/.325/.436 with 30-35 doubles, 18-22 home runs, 125 strike outs and 20 steals.
Eaton, on the other hand, should get the chance to win the starting CF job this spring but if he struggles, the Diamondbacks have plenty of other options to go to, including Gerardo Parra or A.J. Pollock (whom I firmly believe has been passed by Eaton on the organizational depth charts). I don't think he'll struggle too much, and even when he does, he's still their best leadoff option because he still gets on base, but its something to consider, especially for short-term fantasy purposes.
I think Eaton is a better bet to be slightly more productive this season (especially if you're looking for steals) and it may be 50/50 that he has a better career. But he won't be an all-star, at least not very often, and Marte could be a star if he puts it together. The decision comes down to risk/reward for you.