I don't know what tools you are using, but the Tegra 2 is substantially slower than the Galaxy S2's Exynos (both in CPU and GPU), which currently has the fastest SOC for a smartphone on the market and the second fastest GPU (after the SGX 543MP2 on the A5 of the iPad 2). Quadrant, BTW is an incredibly unreliable benchmarking tool.
Cyanogenmod is generally considered the fastest and most stable of the Android derivatives. It's entirely possible that hardware acceleration was not enabled on your phone or is not working 100%. As for which ROM, do be careful about which ROMs. A lot of these custom third party ROMs are coded by well, inexperienced people who are putting together their first ROM.
Pure Speculation below:
It is probably a hardware problem or driver problem then (I'd bet drivers, but I don't know enough on the situation to speculate; drivers would be my guess because the hardware is theoretically powerful enough to run everything smoothly given well optimized drivers and phone software). If it were an STS software problem, we'd expect this problem to manifest itself on a variety of Tegra 2-based and Motorola-based phones. Phones from the same manufacturer or using the same SOC should share some similar parts and code. So far, nobody has posted serious lagging problems on any other Tegra 2 device. In particular, we are interested in other Motorola based Tegra 2 such as the Droid X2 and Photon.
Other thoughts:
I'd keep the Cyanogenmod if I were you, unless there is something not working that you need. Right now I use a beta build of Cyanogenmod on my phone as well. Cyanogen generally is much more responsive and faster. Depending on the device and what you do, it may also extend the battery life. As I mentioned before, manufacturers generally do an awful job of ROM writing. To be honest, it's sad that given the vast disparity of resources, they can be outdone regularly by a bunch of college students.
Personally, now that I have gotten used to Cyanogenmod, I really don't want to go back to a non-supported device. I'm thinking that Cyanogen support with dictate my future phone purchases.
http://www.cyanogenmod.com/devices
As much as I like having the latest and greatest, Cyanogen to me has become something of a make or break. For my next phone, I am strongly leaning in favor of the Nexus Series, even though I prefer (and currently own) a phone with a physical keyboard. The trend seems to be moving away from physical keyboards fast.
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