Jack and Miranda's loyalty missions will conflict with each other. After completing both, you will be forced to take a side unless you have very high paragon/renegade. If you don't, one loses loyalty and goes back to normal, and you need an extremely high paragon score to talk them out of it (my first playthrough, I wasn't successful with 95% paragon talking them back into loyalty)
Another mission is Tali and Legion - another conflict.
Zaeed's loyalty mission requires high paragon if you choose to save the refinery workers instead of going after vido.
So my suggestion is: recruit everyone, save jack/legion/zaeed loyalty missions for last.