I think it would matter less about the choice between traditional and CGI animation, than about the artistic style. It is more of a question about realistic versus stylized, and if stylized in what way.
I mentioned the animation style in Johnny Quest earlier (the original series not the later crap), which I believe would be a great style to go with.
Stylizations may work, some have mentioned anime, and then there are various American/anime hybrids such as Batman the animated series, the early seasons. If not taken too far these may work. I would not want to see a Star Trek done in the same manner as Batman Brave and the Bold.
This applies and holds true for both traditional animation and for CGI.
Something to consider is that if you go realistic with the CGI, I think it may be better to use live actors and virtual sets rather than complete CGI.
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