Long, long ago, the real biggie was the wizards and swords one. We cured that one when one time the mages and thieves, the sole survivors of a mêlée, started to squabble over the division of the loot, drew swords and axes, and slaughtered each other tout de suite. Then they saw the wisdom of the arbitrary ruling. By the early 90's, it had even become one of the bits of antique charm of the *D&D rules (another thing to dislike about 3e) that made it attractive to pick up AD&D2 and play that rather than RQ.
And nobody liked the fire-and-forget magic system, so we replaced it almost from the get-go.
I can't remember any other focussed little rules that were contentious, though there must have been many. More often it was whole-system things not amenable to single-point changes (bricks über alles in Champions, the system sagging by about 8-9th level in *D&D, the unreasonable effectiveness of mages when played with a little thought in Shadowrun). The nearest to a point problem was with Pendragon (which we used in a Glorantha setting), where no-one liked the number of shots a slinger could get off on an opposing foot-soldier charging at him, a combination of range, rate of fire and movement rules conspiring together, but that was washed way by the other problems with that particular campaign.