None of the writing bothers me, until Leiland's death. (Which, by the way, was very surprising to me, considering his head wound barely looked bad enough to require stitches, let alone cause death.) The whole "they made me do it" and the head-cradling, and afterward the dimestore mysticism and psychoanalysis -- yeah, totally lame. But I rather enjoyed Ray Wise's goofy Bob-isms. Yeah, I know, he was kinda doing the cop-out Pacino/Oldman/Walken thing of laughing maniacally and shouting a lot... but those guys I named are really good actors, and so is Wise. "WOO WOO WOO WOO WOO WOO WOO WOO! [beat] That's a yes," makes me laugh every time. The only choice Wise makes that I don't understand is the totally deadpan "catch you with my deathbag" stuff -- kinda sounds like bad high school Shakespeare. But then again, so do the characters of Bob and Mike -- maybe Wise was just emulating that.
I agree with pretty much all your points on the cheesiness of the "transient spirit" idea. Again, the only time it really BUGS me is during Leiland's death scene -- that, and the way they felt the need to show us Bob's reflection in the mirror about four times in the series, as though we were too stupid to figure it out.
As far as the feminist stuff, I don't know. It's pretty obvious to me that Lynch has serious issues with women in the first place, and can't respect a woman as a protagonist until she's been put in a sexually compromised position of the nastiest order (i.e., raped by her father and prostituted to every man in the northwest, or raped with a pair of scissors and stripped naked in public as in Blue Velvet, or molested in such a way that she ends up "liking it" as in Wild at Heart). When it comes to anything that is declared possibly misogynistic/racist/homophobic, I personally need to play it by ear and see if the thing feels ugly to me. Cooper getting "the last word" sounds like a bit of a stretch to me.
Let's not forget that Lucy's pregnancy -- not just out of wedlock, but with the father in dispute as well -- came almost directly on the heels of a scandal that nearly got Murphy Brown censored and/or canceled for simply portraying single motherhood. It's not Bikini Kill, but it ain't bad.
Finally, I don't think anyone would dispute that Lynch should have directed this one, should have directed all of them, and should have maintained a closer relationship with the series overall. I can only imagine what season 2 would have been like if Lynch had done more than just lay down ideas in between other projects. There wouldn't have been any goddamn human-throwing at Nadine's cheerleader try-out, I can tell you that much.