I think both are going to be fantastic players. Merriman has the edge now since he really plays mostly the QB whereas Ware does a lot of re-routing of the receivers and coverage.
Where I like Ware is that he still has a better first step than Merriman, if every so slightly and has a longer reach (that's why he's able to force fumbles). Merriman's first step is only slightly behind Ware's, but is much stronger and uses his hands better.
Once Ware starts learning the game better, gets stronger with his upper body, and learns a couple of more moves he can be just as big of a factor as Merriman.
I actually kind of like Ware a bit more in this defensive scheme since he's far better in coverage than Merriman (he really struggles at that). But if the Chargers ever went to a 4-3, he probably wouldn't miss a beat and I don't think Ware is a 4-3 DE if the Cowboys ever go back to that.
Rich........