Well, one big thing is that they dropped the simulator after 9.1, which I find very handy. I know, I should grow up and use Modelsim, but I've poked at it and found it non-intuitive. The Quartus simulator is simple and easy to use.
My other complaints are pretty nit-picky, but everywhere I turn in 11.1 I've lost some nice feature and found an intermittent bug in its place. When I invoke 11.1, for example, it opens my last open project but doesn't open my top level design. I tend to do my top level in schematic form, and code the various functional blocks in Verilog. The schematic entry tools are buggy, copy/paste doesn't always work correctly. Double-clicking on a top level entity doesn't always bring up the underlying code, pop-up windows are sized inappropriately so that you have to use scroll bars to reach the various buttons. There are numerous other annoying "features" that make me curse it every time I use it.