I use Legacy and I just use the ANSI format to upload to WikiTree. No GedCom is going to be perfect and you will need to edit each profile you create no matter what format you use, even outside of Legacy. You should be sure to make your first GedCom very small until you get used to working with the GedCompare aspect of WikiTree. Most people start with about 100 or so people on the first try.
I'll be honest and say that I have never gotten used to using the GedCom upload with WikiTree and find it more efficient to just manually create the profiles I want. One thing I do is format my citations on Legacy so they basically are copy/paste to apply them to WikiTree. I do that by using the WikiTree Sourcer and pasting that code in the Overrides section of the Source Detail.