The continuity in Marvel is really, really, all over the place. I have been reading comics since I could read, but being in my early 20s, I can imagine anyone new to comics in general would have no idea where to start or what is going on between the vast amount of titles and series', overlapping and retconning themselves and the Earth-616 continutiy everywhere you look.
What I think Marvel ought to do, is start fresh with a new continuity, the same intention behind starting the Ultimate Universe, but without the intention to destroy that universe/drag some of its original characters into Marvel Prime.
What would you like to see in a new timeline, not as a joke universe but not a part of the multiverse with only one stark difference?