Hopefully, they would keep the loyalty missions and Garrus' mission would involve him in becoming a SPECTER. He always wanted to be one so he could do what was necessary to bring criminals to justice. It would be perfect for him. Everyone else I don't think should even try to do stuff on their own.
About the final level of ME1 and ME2, I loved both of them. In ME1, once you are done talking with Virgil, you pretty much go on a wild ride to and through the Conduit, arrive at the Citadel, and then make your way to the council chamber all while a battle takes place between the geth and the council forces and Sovereign looming before you and the Reaper gets bigger and bigger every time you see it. Then you fight Saren, Sovereign is destroyed, and the galaxy has been saved.
In ME2, the final mission is more focused on humanity. On the surface, it was a human problem. The Collectors were only abducting humans from the colonies in the Terminus systems. Once you get to the Collector base, you see that they are using humans to create a Reaper that looks like human for some reason. The Collector base mission was epic and fun and it enabled to actually let you make decisions that could determine who lives and who dies. Then you fight the TermiReaper and the day is saved.
Although the final mission was fun, it really didn't push the narrative forward that was set in the first game. At the end of the first game, we know that the rest of the Reapers are coming. At the end of the second game, they are still coming, now we just know that they are coming at conventional speeds and will take a really long time until they even reach the edge of the galaxy. Instead of abducting humans to make Reaper babies, the Collectors should have been working on building another Relay that could connect to dark space. I think the recruiting could have been handled better as well. The recruiting should have had something to do with the main plot and then you do their loyalty missions.