I'm wondering if, perhaps, the reason why 1080p is so stuttery (and possibly why Apple locked it off in the Apple TV) is because the CPU might be too weak to handle 1080p consistently? We must remember that as much as Apple likes it being branded as the "A4 processor," the CPU is not their design at all; the "A4" is just a four-chip package: 1 CPU, 1 GPU, and 2 RAM chips. Currently, while they designed the package, the chips themselves are very, very standard.
The CPU contained within the A4 package is an ordinary ARM Cortex-A8, the same as used in countless other smartphones. The clock speed for it can vary, up to 1 GHz, as is used in the iPod Touch and iPad. The A8 DOES have SIMD capability, giving it much better media-playing capabilities than older designs, (like the ARM-9) I question if 1 GHz, given the relatively low performance-per-clock ARM has compared to desktop architectures, (such as x86 CPUs from AMD and Intel) would be capable of handling 1080p decoding at full framerate.
Hence, if that's the case, then I wouldn't blame Apple for disabling support for 1080p; it's a consequence of them using a too-weak CPU. Instead, Apple should be blamed for cramming their A4 design into everything they can find, (next up: A4-powered iMac!) rather than using a more properly powerful CPU. Really, hardware-wise, the A4 is a DOWNGRADE from the previous one, a 1 GHz Pentium M. Ditto goes for the RAM (which goes from 400->333 MHz) and the GPU (switching out a GeForce Go 7300 for the SGX535, which Intel also uses for one of their GMA chipsets...) and the internal storage. (from a 160GB HDD to 8GB of Flash) That's right, a downgrade across the board.