CODA is, probably, the best of the actual systems but it's almost like Decipher wanted to hide that there was a game in all the random Trek stuff that they throw at you. Character generation is all over the place, and explanations aren't given in a rational or consistant manner. Once you get past that, though, it's a lot of fun to run and play with.
The major downside with Decipher's handling is that TOS is really an afterthought, with much of the attention placed on DS9 and VOY (the then-current shows). The attitude can be particularly glaring at times with "Run it like a TNG script, only make everything suck more".
I generally found that using the CODA system with the LUG and FASA versions of the Trek game providing your background fodder gives you the best 'metaverse' from which to run Trek.
Mileage, of course, varies.