I am also having this problem. My ATV2 is connected via Ethernet. I tested said connection on my laptop and I'm getting 25mbps down and 6mbps up no problem. I connect it back to ATV2, try to stream one of my purchased shows and I get PAINFULLY slow performance. 55 minute wait for a 22 minute show? HD or Standard shouldn't even MATTER at 25mbps per second (that's over 3MB per second download... =P).
I noticed that iTunes on ATV2 is generally slow to begin with (since I switched from unstable-Wireless to hard-wired Ethernet). When I freshly purchase a show, it'll load for a bit, then start playing before any decent amount is buffered, so I just get constant freeze-playing going on. If I stop the show and try to Resume from where it left off, that's when I'll get up to 3 hours load time estimate on my 22 or 45 minute shows.
Last night, it was behaving this way, but at random moments when stopping the premature stream and trying to start it again, it would play through at proper speed (where buffering was ahead of the timestamp) and would actually flawlessly download/stream the whole show no problem.
It sounds like Alia's problem where after 11:30pm it all worked normally again. But it was eratic. Streaming didn't improve based on what time it was for me... I always had to start a stream, cut it, try it again... and if it didn't work or gave me psychotic load times, I'd cut it and try streaming again. It was hit or miss, but it seems like it's a problem with the iTunes server rather than anything else. YouTube and Netflix run flawlessly. Even airplay worked fine. It's JUST iTunes that was unreasonably slow... it even took longer than it should to load thumbnail images or just to connect so that I could even VIEW my Favorites.
Is there something wrong with my Unit itself? Should I take it to the Genius Bar? Or is this a server-end problem for Apple that we just have to wait for a fix?
As for throttling... I'm on Comcast and there's no throttling going on.