I suggest adding the following to your list:
Ultimate Spider-Man Essential Dr. Strange Vol. 1 Essential Spider-Man Vol. 2-5 Essential X-men Vol. 4
As for the newer stuff, everything in the Ultimate Marvel Universe (a restart that is 'inspired by' but needn't follow the regular stuff) has been collected in trade paperback format (with the exceptions of the latest issues, which will be released, but not yet.)
For the mainstream books, I really enjoy 'Exiles.' That's had four volumes released already, with a fifth to come to comic shops in September. (Bookstores like Amazon are often a bit behind. They were two months behind on volume four, due to Marvel's distribution methods.)
As for filling in the gaps between then and now, yes, there are a couple of decades and creative teams between the most recent Essentials and the current titles. (The Spider-Man Essentials go up to issue 113 or so, and issue 500 ships in October.) There are a few good 'jumping on points' in between. I've found that the Essentials cover the first appearances of most major Marvel characters, and that the missing pieces are fairly easy to pick up on. Go with what interests you.
Also, my tastes may not exactly match yours. If you head over to
http://www.bureau42.com and use the 'search' feature, you'll find my reviews of everything you said you've already read. Comparing my opinions to yours on these works, and the stuff you haven't read, should give you a good feel for what's out there.