BMW tends to pair an engine with a particular transmission. The N20 engine used in the 28i models was designed with the 8-speed because it is a new engine just recently released in January 2011. On the other hand, the 35i model uses the older N55 engine which dates back to late 2009 with the E90 architecture in the 335i. While I realise that the N55 is now paired with the 8AT in most other BMWs, I'm sure there's probably some packaging limitations in the X1 due to its smaller size and shared architecture with the E91.
The 8-speed is a more advanced transmission. More efficient, shifts faster, and more responsive. Maintenance-wise, both are costly and complex to repair. Both are ZF-built. I'd just get the 28i with the 8-speed autobox.