I've always found it quite limiting that the main plot in previous titles was geared toward good characters.An option to work against the Septims in Oblivion would have been a nice addition for example.Even if the plot was unsuccessful for the sake of the games lore it would give the less reputable characters something to get involved in.
The mages guild questline in Oblivion is another good example where the battle with the necromancers was never fully explored or taken advantage of.I could probably add the fighters guild questline involving the blackwood company.
Any thought's?