Been there! When I started, I could not imagine recreating 4000 people just to be part of WikiTree, especially after spending 25 years fighting other rather dismal software venues. It was infuriating to step through the awful GedCOM alleged "matches" one by one. And I didn't even yet know if WikiTree would be an improvement! Was I wasting my time?
Then someone told me to just ignore GEDcompare and fix up the profiles already entered. I found then that creating the rest of the tree was smooth, not that painful, and that I connected up in several places rather quickly. (Yes, a few times I blew it, created duplicates, and had to fix them up. Things happen.)
So, for what it's worth, I'd say that I'm glad to have stumbled through that process. I think that WikiTree is worth the frustrations. The community is more than helpful and can be fun.