I'd put Enterprise above Voyager, mostly due to Janeway. Not because of Mellgrew or being a female captain but because she struck me as a Star Trek Hermione Granger, an insufferable know it all. I often found myself wondering why she had a crew. Robert Picardo was the one saving grace of Voyager for me.
Another reason I side with Enterprise over Voyager is that it broke away from the Roddenberry optimistic view that the STU Federation was exceedingly peaceful. Much of Enterprise predates the creation of the Federation of Planets (if memory serves me correctly) and while there was the beginning of the Prime Directive being observed by Archer and the crew, they were willing to suspend their morals when the fate of Earth was in the balance. Very much like the DS9 episode 'In the Pale Moonlight', probably one of my favourite episodes of the entire franchise.