To your points...
-Voyager... yes had a lot of filler episodes as you said. But what made DS9's user of filler so much better was it was relevant filler. Voyager usually just pads out scripts with either endless technobabble or scenes about how awesome Janeway is supposed to be.
-About the aliens, to be fair... they were flying home so most of the aliens really don't get a chance to get explored. The Kazon did and were obviously lacking. The same with the Talaxians and Viidians. If Neelix was a typical Talaxian I can't feel too bad about their homeworld being occupied.
The Ocampa were a huge missed opportunity. Despite how crazy weird some of their racial aspects were, they could've been really explored through Kes, but weren't.
-Well the humans with funny forehead aliens are a recurring Trek theme, and one Voyager just embraced. Can't really rip into Voyager specifically for that one.
-Janeway... oh I could rant about her for hours. Really the biggest flaw is the writers seem to have this tendency to put her into manufactured moral dilemmas where it's "I'm the captain and I'm making the call" as a way to compensate for her being the first female captain. In reality they usually just make her look silly, insane or into some sort of parody.
-Haha! I'm a strong advocate of the theory that Janeway had Chakotay neutered and that's why he's so mild and tame after the pilot. But if Kate Mulgrew is to be believed, she's the reason they never got together. Mulgrew said she didn't think it would be appropriate for her to get involved with a subordinate. So instead she dates a Gestapo agent later on instead.