For example, the luma levels vary. Encounter at Farpoint is pretty good, with black usually being black. But I was watching Unification last night and black was grey.
The blacks are all over the place, especially in the later seasons. The frequent cave scenes usually suffer, and the MPEG compression is noticeable at points too. I think DS9 thankfully tended to look better on DVD, as it was generally lit darker than TNG. I can't comment on the Voyager discs, but I imagine they look better than TNG too.
The DVDs generally look fine on CRT, but LCD displays are very unforgiving to any sort of VT-sourced programme.
And there are really some very poorly transferred effects shots with what looks like combining. Also some of the effects shots are telecined 24fps but others are 30fps interlaced video, and it seems that the two are interwoven or just messed up in some way!
Yes, that's part of the problem with the way it was edited rather than the DVD transfer. Another big advantage of a full remaster will be to iron out these dodgy VFX overlays. I think it could look amazing given enough time, money and expertise.