After reading into it a little more, it seems like the lack of grade separation had more to do with a lack of funds than it did with oppsition from the Sierra Club.
I think the environmental groups were pushing to have transit included in the plan (which they got), as well as the air filtration for systems for elementary schools and the relocation of an entire school in WVC (Which I think is stupid. I went to gradeschool next to a freeway and I didn't die of pollution at recess, neither did any of my friends.)
Overall, I think that UDOT has been pretty progressive as of late, and I hope that the state/feds can come through with some funding to finally get this thing started. (Maybe we could get Dolan and his lobbyist friends to attach its funding to some bill in congress, just like with the money he got for 1300 E. in Sandy

)