I was mostly dissapointed about how the council outcome was handled post -ME1, for one, ME2 doesn't differentie between the paragon/renegade variants, this is especially bad when the council was sacrificed, where it is confusing whether we're dealing with an all-human council or a human-led council.
When we finally do get to meet the new council Mass Effect 3 all the conext of the orginal decision is gone, there's just three new council members and that's, it, their dialogue is different, sure but their role is very much the same, the choice doesn't make any difference on the progession and tone of the narrrative. There is no sign of the human chairman, no sign of increased animosty between the old guard and the newcommers and no sign of having made a difference at all, well except war assets.
Oh, and if you saved the Council you get an extra shot of the Destiny before the final battle (though you will never see it in combat, because of generic scenes with absurdly high amounts of human ships), and if the council died well you just get a generic asari cruiser, they have to show you something after all.