I kind of agree with them scrapping the original version of Thessia because it would have required two mandatory squadmates on that mission. I'm okay with having one mandatory squadmate on some missions, but two would be a bit much for me. Also between that version of Thessia and the Coup the game would probably be putting the VS on the chopping block too often.
I kind of wish they had something like ME2's suicide mission for the end run of Mass Effect 3, except with all of the surviving ME2 squadmates joining for the end run and being selectable as well (like the arena in the Citadel DLC), and with there being some unavoidable casualties. Having said that I also wish the ending was quite different and worth the sacrifices the team would make in getting there. But that's a whole different discussion, and dead horses and all that.
The VS still wasn't a squadmate at this point in the story. And it was only scrapped because of a lot of little surrounding stories -- especially Javik. They had to rethink Javik because they were running out of time... and then they just salvaged what they could of him as DLC.
Basically though, Ash or Kaidan kind of become the hero of their own story once they become Spectres. They are investigating Prothean stuff, and you run into them twice, I think. Once at Eden Prime (which goes badly between you and them), and finally at Thessia. The kicker is that Kai Leng is with part of their "squad" posing as some Alliance rep (i.e. like maya brooks), feeding ideas into their head that you can't be trusted and you're still with Cerberus. Once the jig is up, Kai Leng finally forces a Virmire like situation between the VS and Liara, and gets away.. just like Saren did. And afterwards, you get Javik.