The difference, as it pertains to the patent issue, is nothing technical - it's simply that Intel feels threatened by Microsoft's emulator and not by qemu. (Though if Intel has ever redistributed qemu, there may be an additional GPL wrinkle...)
Intel contributes to qemu (or at least, developers with @intel.com email addresses contribute). However AFAIK they don't contribute to the emulation code (TCG).
I quickly watched this and they seem to be running a jit with disk caching. Also they had League of Legends on the desktop so i'm guessing they support sse instructions.
Market size. Intel can choose to sue or not sue. There's no obligation to chase after every infringement, so the ones they do chase are picked by bean counters.