Umm... have you been on Dr. Diabolical? While I'll grant you the ride itself isn't super themed, it does have some very fun voice narrations. But the queue? Crazy themed with two pre-show rooms that include electronics and story-telling. Blew me away. They also did the same crazy queue theming for their version of Crazanity... it's a full blown fun house queue. Same for Poltergeist (as you mentioned) and the Pirate 4D shooter ride. So SFTT is not exactly hurting in the theme department, especially for being a Six Flags park.
I can't imagine Viper ever getting a lap restraint... has any Arrow coaster ever swapped out OTS for a lap bar? But I defintely wouldn't mind the vest restraints. And while we're speaking of Viper, I rode it about a month ago and was totally shocked at how (relatively) smooth it was. Not perfect by any means, but the smoothest I've experienced it for a while.
As far as the "deforestation", I figure that's an ongoing reaction to the branches that fell on Ninja. I figure the park just doesn't want to risk anything like that again in the future, but has gone a bit overboard IMO.
I wholeheartedly agree with you on more flat rides, though. Been saying that for a long, long time. I feel like SFMM is one of the few SF parks that hasn't received a flat ride package, and it's arguably the one that needs it the most.