I love the Xindi arc. It's my favourite season of Trek - I couldn't wait for next week's episode. It brought back the ass-kicking adventure that had been missing from Star Trek since the TOS movies. And the Xindi were fantastic aliens, far more interesting than Klingons, Romulans and Suliban.
Although yes, it very much has a made-up-as-they-went-along quality. Why test a weapon on Earth and alert them? Why the need to build a steampunk Death Star and blow the planet to smithereens when you just need to eradicate all life on the surface? How does Earth destroy the Xindi homeworld 400 years in the future when we learn the Xindi destroyed their own world 300 years ago?
As for the Space Nazis at the very end, they didn't bother me one bit. Of course
time-travelling aliens were involved in WWII! That kind of stuff is a given in Trek. Mark Twain knew Guinan and had to deal with soul-sucking weirdos with a snake-cane, Brahms/Da Vinci/Alexander the Great was an immortal alien who met Kirk and Spock, Zefram Cochrane got stuck in the middle of a future war between the Borg and the Next Gen crew... of course aliens were it league with Hitler.