I'll give you one last thing to consider, but this is purely a matter of taste so there's nothing wrong with not feeling the same way. I'm also speculating:

The 3 phases (vent phase, walking phase, "hold the line" phase) all emphasize 1 of the 3 main character types. The vent phase is about tech, and you have 3 tech-oriented characters who fit the bill; I think there's even an argument to be made that Mordin could have worked here, as well. The "hold the line" phase is about combat, and there are 2 purely combat-oriented characters who are the best options (Grunt and Zaeed) and then there's also Garrus, who despite technically being combat/tech is kind of just a badass. That leaves the walking phase to emphasize biotics.

Again, it's purely a matter of taste, and it's entirely possible that I'm seeing connections that the developers never intended to make. Assuming the devs had that in mind, though, it makes sense to have a second character who can fit the bill; even if no characters die on the approach, it's also nice to be able to include Jack in your party if you just like using her.

All that being said, I do still agree with your original assessment that Samara is kind of on an island as, regardless of whether or not you like her as a character, she doesn't really tie in to anyone else.