I think EVO is the best of the three. You can do a whole lot of things on one pilot file, the galaxy has a lot to explore, the ships are brightly coloured and actually make you want to buy them!
Also, comparing to Nova, you don't have to spend most of your time reading and not so much playing! And combat in EVO is far more close-up (as it should be in EV games IMO) - I really can't get interested in the "I-can't-get-close-enough-to-kill-you" fighting in Nova. It seems to me that all the stuff about improved AI really means just that it's pretty hard to get in range.. once you do it's no problem.
Capital ships in EVO were a lot more powerful than the rest - I think that was a lot more realistic than Nova where most ships can be destroyed quite quickly.
And finally for now, the galaxy in EVO is more sensibly designed - if I want to go somewhere I head in that direction - generally without worrying about dead-ends. In Nova, especially Federation space, the design gets incredibly annoying and unnecessary - especially when you don't need to go to most of the places anyway.
Basically, EVO built all of the races' cultures remarkably well in the not-too-long mission strings, planet and bar descriptions, without going overboard. For a galaxy with well defined government boundaries, I'd far prefer to live there than in the Nova world.