TNG is my favorite Star Trek.
Honestly, I did not like Voyager. It was a good show, but Captain Janeway is by far the worst of all the captains. Its something I noticed, but women who like Star Trek (no offense Shelly), often think that Janeway is the best captain... most likely because she was a woman and they are supporting their sex. =P
That being said, my problem with Janeway is the fact that she was a terrible leader. In one episode, the Voyager crew could stumble accross a neolithic civilization being oppressed by another, and Janeway will spout off the prime directive and non-interference. Then in the direct next episode, the exact same thing will happen and Janeway will go all gung-ho "**** the prime directive!".
She flip flops and can't stand by her decisions. Hell, her indecisiveness is the reason why Voyager is stuck in the delta quadrant in the first place. Every civilization Voyager makes contact with, ends up destroyed by the end. Naturally, this isn't Kate Mulgrew's fault, she is a great actress. But this is the fault of bad writing.
http://blair.mitchelmore.ca/captain-janeway-destroyed-star-trek/
http://fullphaser1.wordpress.com/2010/04/30/captain-janeway-is-the-harbinger-of-death/