I'm of the school of thought that's perfectly willing to give SM a darker feel 
to it.  It's a change from the saccarine, made-of-ten-year-old feel of some 
parts of the series.

Keep in mind, the manga was several shades darker than the anime.

We have no idea how long Usagi was acting like that, that sort of thing can 
happen rather gradually.  It was as if Ami had taken a step back from 
the present & compared Usagi to the original impressions she had of her.  A 
change that took years, and could be in character for the decidedly 
more-twerpy Usagi of the manga.

As for Mamoru playing musical beds with Ami..
I doubt he was ever really out of love with Usagi.. and I suspect all the 
Inners have feelings for Our Pal in the Tux.  As the writer of 'Anniversary' 
pointed out, a thousand years is a *long* time to be looking at the same 
person.  Who knows *what* the Senshi are up to afterhours H_H (seems the Hentai 
Side is being vocal today...)

As for Setsuna...
How often has Setsuna been some wierd hybrid of human & alien/demon/whatever in 
fanfics?  Doesn't it make more sense for there to be one Senshi of Time who's 
origin requires time travel?

Ah well.. maybe I should change my name to J. Random *Opinionated* Fanboy ^_^