Here's my solution - I hope it helps at least a few of the people here or points them to a solution for their own set-up.
I've been following this lengthy discussion ever since I first had problems with a migration from ATV 2 from ATV 1.
The ATV 1's always worked pretty much perfectly (with only occasional buffering issues) but as soon as a I switched to ATV 2's I couldn't stream HD or SD movies via the ATV 2's without the constant stop and start of buffering or indeed as many people here have reported not even getting to the point of playing. I'm thinking that the ATV 1's worked because of their internal hard discs which the ATV 2's don't have and this helped with the buffering.
As a temporary fix I was using a Mac Mini as an iTunes server (which serves my audio and photo collection to the ATV 2's plus all my ripped DVD's & Blu-Rays). Using this server I would rent or buy HD movies from iTunes and then stream them from the server to the ATV's without problem although this approach kinda defeats the object of having an inexpensive ATV device.
That said this set-up gave me a clue that something was wrong as I would get strange and wildly variable download times after purchasing a rental or movie. Sometimes the download would stall for a while and sometimes it would suggest very long download times for a 3Gb file such as 20 hours, etc. I found my stopping and starting the download on the server or switching my router on and off things would speed up for a while and so on. So these were clues that something wasn't right.
This was despite a 50Mb cable connection provided by my ISP in the UK VirginMedia. Every other streaming system was working including YouTube, NetFlix, etc but as other have pointed out NetFlix uses a different streaming approach that shapes it's transfer rate & quality based on what speed you have so if there is a glitch in your set-up you may not notice it as easily with NetFlix.
Anyway with the help of this forum and others I eventually arrived at a solution that has fixed my streaming problems with the ATV 2's (and I suspect this will work with ATV 3's). It may not work for everybody but it may point people in the direction of a solution. It's a shame that the ATV isn't plug and play in the way that I feel a consumer product should be but here we are!
My set-up
VirginMedia cable 50Mbs using their SuperHub router.
Time Capsule (TC)
Airport Extreme (AE)
2 x ATV 2
2 x ATV 1
So, after a lot of experimentation, this is what eventually worked and is now flawless:
I disabled the Flood Protection and IPsec pass-through features of the routers Firewall protection and put it into modem mode.
The TC was then connected to the Virgin Media cable router (that was now in modem mode) and became the router.
The AE was used to wirelessly extend the network to other parts of the house (it's a large/tall Virctorian terrace house!)
I downloaded version 5.6 of the Airport Utility and then downgraded the firmware of the TC and AE to version 7.5.2
I have one ATV 2 connected via Ethernet to the TC in my living room and the other ATV 2 and two ATV 1's are distributed around the house and connected wirelessly to the network.
They all work fine and often simulataneously given we have kids etc.
The 1st "break-thru" moment in this journey was the disabling of firewall features in the cable router which solved most problems until Apple upgraded their AE/TC firmware to 7.6.1
The 2nd break-thru was discovering that Apple's AE/TC firmware was messing with the set-up. A quick downgrade and then, like magic, everything worked.
I don't expect this to work for everyone but it worked for me and I did set things back (especially the AE/TC firmware) to double check that it was really this that was causing problems.
My guess is that something in the Firewall protection in the original router was preventing the ATV 2's to stream in the way they want to and that there's a similar problem in the latest AE/TC firmware or a combination thereof - either way this still seems like alchemy and not something you'd expect from a consumer product from Apple.
Good luck everybody!