I've been thinking, did anyone ever consider actually re-shooting the FX-elements with full-size replicas of the original filming models, using the original film stock etc., only to composit it with modern software? I would LOVE to see the results of such an endeavour. I bet it would look stunning.
That sounds like a terrific idea, but it would be too expensive for the budget CBS allocated for the restoration of the original series.
Well... the biggest problem I had with the space effects were how overlit they were. It seemed like someone was always had a light shining on the Enterprise. It ended up making it look cartoonish and didn't match the live-action elements.
Some of the digital effects are definitely over-lit, especially in early episodes. (I think the Blu-Ray even has a comparison of the Enterprise in early episodes versus its appearance in later ones, in which the lighting is much improved). Having said that, if your problem is effects that were too bright, I'm not sure how well the originals hold up in that regard.