I'd love to see the following features added:
1) The new "We have located [N] temporary files" feature is utterly annoying. I presume there are lots more people like me who keep their temp files under control and don't want indiscriminate removal (even automatically, if you don't say "No" in time!) of them by any program whatsoever. It really should be possible to enable/disable this feature under Advanced Mode / Settings.
2) It's a pity that you can't pause Spybot (like you can pause e.g. Win defrag). I've run into this problem several times with older machines, especially laptops, where cpu cooling is problematic. On one particular laptop Spybot could never complete a full scan, because the cpu overtemperature protection powered down the machine. Adding a "Pause" feature would make it possible to run Spybot on such machines too.