Personally, I would like a mix of both. I really do like the stock missions, as they are usually quick and when you are doing hours of hex flipping its nice to have them quick and painless.
However, I do think a 60/40 mix should be used. I intended to use a few of Karnaks on LB5 if he had finished them before he went on vaccation, but alas it was not to be, and I wont have a buggy server. I want some of the complexity that NW puts in his, and the AI stripping that Karnak does, and I like some of the neat features that TraceysG's do, like the medals and such.
Given a little more time, I think all the scriptors will get things going in the right direction again.