Speculating on what Gene Roddenberry would have liked or not liked about Trek since his passing seems to be a favorite pastime, often colored by folks' personal perception of the man...
All that being said, I'll throw in my 0.02--I think Roddenberry would have been pleased that Trek is still around in 2009 and seems to have a future. He might have had different opinions on individual productions, but as a whole, he probably would love the idea that his creation is still ticking and is still celebrated by fans.
Anything else is usually the general trappings of doing business in Hollywood with disagreements with the studio over creative decisions and control, giving credit where credit is due, etc., and Gene Roddenberry was by no means the only one to have done stuff like that and to sometimes come out villainized by it, IMO...