Having two or three companions doesn't matter that much to me (although three would be nice), what I would prefer instead is:
- More banter between companions during missions! This is an awesome way not only of getting to know the characters themselves, but also their relationship with the other members of the crew.
- Being able to "assume direct control" like you can in DA and switch between companions. It feels weird that the moment Shepard is incapacitated the mission fails; I would like it if we could keep on playing as the one of the other companions. The thought that bad-asses like Garrus and Jack would have given up the moment Shepard was unconscious is just not plausible.
- Missions where the other companions are present but doing something else off-screen. Like others have mentioned, why leave so many competent people behind all the time? It doesn't always have to have a big impact (like ME2's suicide mission), it would be enough just to hear some radio-chatter between the companions.
These are just my wishes though, and I'm guessing there are reasons why some of them are not implemented.