Then there's the aforementioned possibility that classic will not only hang, but that it'll hang in such a way that you cannot start it again successfully without rebooting the machine. Not fun, especially considering the current dearth of native OS X applications. I've also found that it helps to shut down classic at the end of each day rather than allowing it to sit idle over night, but your mileage may vary. Integration with the rest of Mac OS X is impressive, given the technical hurdles. Given the incredibly buggy and decidedly non-integrated state of classic in many of the development releases, the integration of the 10.0 incarnation is a pleasant surprise.
Cosmetic issues abound.
Classic is not double-buffered like native OS X applications, and it shows. They're quickly redrawn, but not quickly enough to remove the incredibly ugly effect. Transparency also doesn't work when displayed on top of classic applications. This includes menus, the Dock, and anything else non-opaque that can potentially be displayed on top of a classic application's window. In reality, it is slightly slower on the redraw in almost every respect.