It's been a while since I've played, but I remember that I failed Zaeed's loyalty mission my first playthrough because of it. There were also times when I reloaded because my LI got mad at me for picking the stupid moral high-ground choice where it was clearly not appropriate. I think that choosing the Paragon option in Legion's loyalty mission also has repercussions in the third game. I do agree with you, however, that there should have been more times when choosing the few over the many came back to biteme in the butt.
Well, with Zaeed, it was simply a matter of persuading him that doing the right thing was the best course of action. Which was possible with a high enough Paragon level. If you always chose the Paragon path in every instance, this will work out in your favor - although I'll concede that is more of a flaw with ME1 & 2's persuasion skill system than it is a morality system issue... but the fact that the two were tied so closely together encouraged (although certainly not required) the player to stick with one morality.
And I believe the Legion's loyalty mission was a wash. Rewriting the Geth gets you more Geth Prime War Assets, destroying the Geth gives you more Quarian War Assets (the thought being that the Geth did less damage to the Quarians during the assault before Shephard arrived). In terms of story or your options for negotiating peace, I think it was minimal.
To counter my own argument, though, I can think of one instance where the Renegade option was beneficial - Garrus' recruitment mission in ME2 allowed you to assassinate the mechanic working on the gunship that would later attack you. With that one Renegade act, that fight becomes much, much easier. Easier fights aren't something I value as a choice consequence, though. The same can be accomplished by going into the menu and changing the Difficulty menu. I'd rather see something narrative or plot based in consequences - that way it feels the world is being impacted, rather than the only variance being my experience, as the player, becomes less challenging.
But that's just my own two cents.