1: They age horribly. I was watching What You Leave Behind a few days ago and I noticed in the last scene when the camera was panning out from DS9 to outerspace that the station was obviously CGI. Watch Lord of the Rings.
2: They look to fake. Can't capture human emotion properly. The scene in First contact with Picards eye or in DS9 when the camera was focused on Ezris eye had more range of emotion in it then an entire episode of CG can.
Many effects look dated. I mean I see many Star Wars fans DEMANDING the pre 1997 original triliogy on DVD, but that's gonna look REALLY horrible in DVD format. Plus the original SW effects, before 1997, looked horrible to me.
And CGI can be great in many ways. Take Dr. Who for example...the BBC trashed alot of the episodes in the 1970's, and some are totally gone. With CGI, we can make the episodes come back, since the audio tracks are intact for all the episodes, and I'm sure that getting the general idea how it looked can be done from still shots, photos, and storyboards. Also, CGI can be used to make more 'classic' Dr. Who stories, using the actors that are still alive.
Here's 2 great examples CGI can be used for.
With a lil more refining, and some improved touches, I could see awesome stories in each example.
Plus the idea of seeing THOUSANDS of Daleks is fun.
So, I can see Trek doing the same. I like how Aurora looks there, and would easily watch something like that.