Intel hyper threading increases throughput because having hyperthreading is better than nothing and doesn't cost much die space. However I'm afraid this increase is still not as large as adding a couple more physical cores. Is AMD's architecture slower per-core? Yeah, a little, but with magny you get 12 real cores instead of 6 real cores + HT, and you get very respectable performance with that in most areas, and better-than-gulftown performance in a few niches.
It's a pity that anand's IT benchmark suite is so dull, but you can see magny, with a 700 MHz clock disadvantage, doing some serious clean-up in the very-parallel work like rendering and fluid dynamics. I wish we could see more workstation and less server apps, though. Something more serialized like a database benchmark is going to just go straight to intel. Their core is simply faster than AMD's and thats the way it's been for a long time. Throw a 700 MHz clock advantage on top of it and yeah, it's better. It may not be explicitly written down in intel's strategy, but they are holding onto the fastest core, they have the best performance per thread and they're keeping it that way.
AMD just has a lot more physical cores and they are clocked a little slower, but it brings definite victories in some areas. There are two distinct, but easy to understand strategies that intel and AMD have chosen because not all work computers do is the same, and you can't have a best-for-everything architecture. Was AMD supposed to just not pursue this strategy? Were they supposed to keep copying intel? That would still leave these embarassingly parallel niches unoccupied.