The decks I like to play the least against in Modern:
1. Land Destruction. Luckily Wizards got the memo on these and the format is very unfriendly to successful LD decks. Legacy is another story.
2. Storm, and other 'all Solitaire' decks like Eggs. Storm is still around, and Wizards also got the memo on these. Eggs is no longer viable, but every now and then I face one of these decks in Modern Just for Fun.
3. Origins Jace and the mono-blue control extra turns everyone draw cards decks. Origins Jace is not ban-worthy, but it tops the list of cards that are just below that threshold. Wizards has not gotten the memo on this one, especially since so many articles they publish are of the type 'hey, everyone has a play set of Origins Jace, or should have one, here is another deck in which to use your play set.'
4. Mill. And this one is a distant 4th. 1, 2, and 3 above are really the ones I would love to see go. 1 is gone, but 2 and 3 are not gone.