The second game makes sense, at least with smaller missions. I imagine Shepard would want her entire team for bigger missions, like Horizon, Collector ship...
Come third game, I imagine the entire team would be deployed most of the time, unless it's smaller missions again(like ardat-yakshi monastery).
I see it more as limitation of game engine and imposed challenge on the player. If you could bring entire team on the mission, this would be closer to Commados or Desperados, or maybe X-Com style of a game. And the game would get quite easy too fast. But for me too, it makes more sense than more than just the three people we see are deployed most of the time.
Late reply on this one

Shepard's henchmen number can be quite limited. If you only get the mandatory ones, the list can be:
ME1 - Kaidan/Ashley*, Liara, Tali
ME2 - Miranda, Jacob, Mordin, Grunt, Jack, Garrus, #7, #8**
ME3 - James, Liara, EDI
*Only one makes it to the end stretch of the game
**Thane/Samara/Tali/Legion/Zaeed/Kasumi, and then with Suicide Mission you can cut this number down significantly, if you do missions/sidemissions after it
So I think that's what the story design generally runs with. Anyone beyond these characters is sorta
extraneous.
In ME1, this means that we can only imagine Shepard having a couple of people with him.
In ME2, this means that at most (hubs? larger missions?) we can imagine Shepard having a few to several with him. An example may be the (silly) shuttle before the Collectors attack the Normandy SR2. It certainly wouldn't be able to fit 13, but max 9? Hmm.. maybe.
In ME3, like ME1, this means that we can only imagine Shepard having a couple with him.