i am coming from the Atrix to the Thunderbolt. i used the Atrix for 4 weeks. i'm not a big gamer but for the little time i played, the Atrix is faster. one example is Fruit Ninja THD on the Atrix never lagged. on the Thunderbolt, i have seen the non THD version of the game lag especially when bonus flashes pop up on the screen.
in real world everyday use though, i don't really see much of a difference between the two phones when navigating around the UI and web browsing. yes, as fast as it is, browsing on the Atrix still gets quite laggy that is so typical on most Android devices.
the main problem the Atrix has is the wake up lag. when i press the power button, it would take 1 or 2 seconds for the screen to turn on. once the screen has turned on, it takes another second or so for the touch sensitivity to wake up so i can actually swipe to unlock the phone. the touch sensitivity just wouldn't respond the first few moments after the screen is on. with my Nexus One and the Thunderbolt, touch sensitivity is functional even before the screen is actually on. i don't know exactly what's causing that problem on the Atrix but i looked at some Motorola Droids in the Verizon store and although their specs are much slower than the Atrix, none of them has that problem. they're all instant on.
it might just be a software compatibility issue with the Tegra dual core CPU. the Atrix is indeed fast in gaming and benchmark, but it's very hard to live with that wake up annoyance especially since i experience it EVERY TIME i turn on to use the phone. where as the Thunderbolt's lag in some games is not as big of a deal for me because that is not nearly as frequent of a problem.