I didn't hate the loyalty/influence system.
I hated how it conflicted with the Light/Dark Side morally system...
One touted feature of the system was that you could shift a party members alignment towards your own by having strong influence over them, causing their appearance to shift as well...
Unfortunately, no matter how you shift them, the writing would still script them as their default persona's, which would often conflict with their alignment.
Typical example: You manage to build some influence with Atton. You spend some time without him in the party, during which you decide to throw some space puppies off of a space bridge. Your influence causes Atton to shift to the dark side.
Later, while Atton is in your party, you decide to blow up a space bus full of space nuns, an action that earns the displeasure of a very Sith-looking Atton. He protests "No man! We're supposed to be good people!" as he sheds a tear from one of his soulless eyes.
[i]You've changed man... You've changed...[/i]
Other then that, my other major problem with loyalty in most games is how I can often lock myself out of certain quests or other goodies by not saying what a party member wants to hear, especially when there never seems to be a right answer. I'm looking in your direction, Morrigan...
ME2 did a mostly good job. It makes sense that characters would say "Suicide mission? I'm okay with that, but I have this one issue from my past that I would like to resolve before I put my life on the line." On the flip side, I have trouble understanding how...
[spoiler="Mass Effect 2 Spoilers"]...Tali not being able to visit the Flotilla leads to her getting shot in the face or Samara not completing her mission results her Biotic field failing.[/spoiler]