There's a good reason for that: AE 10.5 won't do it any more.
Oh, there's some kind of roadblock being thrown up by the mpeg2 people, and I forget all the details. Suffice it to say that it won't work any more.
Personally, I view it as a good thing. AE is incapable of doing multipass encoding, a feature that makes mpeg2's look a lot better. You'll get better-looking results by rendering a lossless file in AE, then using that file in Adobe Media Encoder to make the mpeg2.
Actually, the restrictions have always been there. The MPEG formats themselves have very strict constraints. What has changed is that After Effects is doing a better job of telling you what's happening. Note that that message that you are referring to isn't saying that you can't do what you're doing; it's telling you how After Effects is going to convert your movie to what the format demands.
There's more information here.
Why are we all of a sudden restricted? Why would such restraints be put on our MPEGS after we've been using them with no problems for years?
You are merely mistaking some changes in the handling of this stuff. In short: You simply cannot recycle your old settings from previous AE versions as in most cases they will be reset to new defaults every time you open a project, but instead will have to create new output module presets specific to CS5.5 and assign them from there. This is quite explicitly mentioned on the help pages, BTW. Other than that there hasn't been any major change here - as Todd already mentioned, many MPEG types are constrained to specific framerates and resolutions, it's just that the aforementioned change in behavior resets your output to DVD specs.