Very well written commentary lolThey basically had no idea what they were doing, tried to make it Melrose Place in Space with an actress that couldn't act her way out of a paper bag (a scene with bio disinfectant gel comes to mind among many others), then at the very end realized oh fudge we're hemorrhaging ratings, let's try to do a DS9 style war arc (Xindi goodness), but didn't quite pull it off.
It was such a waste for the exact reason they had so much material and some fine actors. I mean T'Pol was irredeemable, but as bad as Merryweather was he got a lot better, Phlox, Malcolm, and Yoshi were wonderful. Bakula hammed it up but he mostly was okay, and the greatest shame was they kept trying to make Connor Trinnear a freaking country bumpkin aw shucks guy when the man was money. The usual suspects of guest actors of course was also good...Shran haha.
Bannon Braga et al. just wasted so much. It was like watching the Oilers with ChiaPet, then with McDavid under Holland. It's passable, but you can be so much more.
I hear what your saying about some of it for sure. The rubbing the disinfectant on each other while in your underwear was nonsensical in at least one episode I remember, and taking a dog on a diplomatic away mission with a species you already offended only to have it take a wiz on a sacred tree?! Yeah that was just a silly story idea imo. They definitely tripped in some story ideas.
But over all I still enjoyed the show. And I really liked T'Pol actually, and not for her "physical" qualities... ahem, I mean I'm not complaining about those qualities, even though every Trek that does that sort of thing is transparent in what they are actually doing. But I thought she played a good Vulcan. Maybe she goes off the rails in later seasons and I'm forgetting?