I don't think Lee was unskilled; yet the fact of the matter is that most of his "successes" were really only "pyrrhic victories," and those are only account of his enemy making severe blunders. Grant, on the other hand, was one of the few generals in the whole war that was an exceedingly good strategist and won campaigns through extraordinary maneuvering and placement. With the exception of the mass surrender at the end of the war, there were only a handful of annihilation victories; all of them were by the hands of Grant. (Which is not to say he's in a complete league of his own with none comparable, nor that he didn't benefit from great luck at several turns; only that decisive victories were possible in the American Civil War, of which Lee scored none, despite being hailed as the alleged greatest in the whole war.)
Lee, I think, is something like the American equivalent of Paul von Hindenburg. Lee had very talented subordinates like Jackson and Longstreet, and since Lee was able to co-ordinate them well, he can be called a good general. But the ridiculous hagiography that the South gave him after the war is obviously undeserved on several counts. Your average postbellum Democrat liked him just because he was the highest ranked general in the Confederacy, and the minutiae of his actual career is irrelevant to them in this regard. But Confederate apologists used Lee as evidence that their cause was righteous, and the Civil War was only lost because the stupider Northern generals had more men to shove into the meat grinder. That's patently false. It's pretty clear to anybody who reads a detailed and objective account of Grant's and Lee's campaigns, that it was really Grant who displayed strategic genius, whereas Lee often applied the "standard" approach, albeit competently.
