Across my many playthroughs, I never lost anyone. I think attributing it to OCD, like someone above me did, will be accurate. I always complete the side quests before storyline quests, and this never failed me.
I personally don't like playing as jerks, so all my Paragon Shepards will have the best start posible, which makes me glad.
That said, there are clues in the game that allow you to make an informed decision as to the order of doing things and final battle assignments.
After the Collector vessel mission (the one that gives you weapon training/specialisation), in the debriefing you discuss whether you should go for the Reaper IFF directly, or stick with building your team, which means, finishing all the loyalty missions.
As for squad members and whom to assign where, if you talk to your crew, you'll find they'll tell you what they're good at and what they suck at:
- Mordin will tell you that he hates "holding the line", preferring to get the job done and go home.
- Zaeed will tell you about many missions in which he preferred to save his own ass and didn't care for others, meaning he might be a good fighter, but crappy leader.
- Samara will tell you how Justicars work alone, meaning she's inexperienced in a leadership role. She is a very old asari, tho, so of course, powerful biotic.
- Grunt is a hormonal teenager and doesn't care much for the imprinting done to him in his tank, but he sure can shoot well and take a lot of punishment.
- Jack will state from the beginning that all she cares for is herself. She can unleash hell with her biotics, however.
- Jacob will tell you he has an experience leading a team. He only mentions his biotics once.
- Kasumi is a techy, stealty chick, but she always works alone.
- Legion can hack everything and shoot really well, but who would trust a Geth leading them?
- Miranda is overconfident and proud, so of course she'd say she's best at everything, but she was wrong on many occasions. The only thing you can trust her on is leading a team, as she actually done it before and results weren't that bad.
- Tali is very talented tech-wise, but she doesn't feel comfortable in leadership role of any kind.
- Thane, as skilled as he is, never even mentions his biotics, and also always worked alone.
- Garrus is more focused on his weapon skills rather than tech skills, but has successfully lead a team of his own, until someone betrayed them.
So there you go. if you were paying attention to what your team says, you can be informed enough to assign them appropriate roles in the final battle.
Now I feel like I spent way too much time analysing it.
