1st Stable code (and beta branch). I know this is obvious, but we need more users in the base to make the technology more trustable and do not mess with production environments.
2nd Rescue CD and the hability to recover the system if something goes wrong with installation, uninstallation, driver loading, incompatible software, infection of MBR, etc. Whatever. You may be able to restore default MBR, reinstall CTM MBR, access the console, access the files, etc. You may also makes feasible the external backup/restore of snapshots.
3rd Multiply platform (at least, dual boot with Linux).
4th Encryption support (as full encrypted software requires the MBR, CTM could control both things).
5th Improve the GUI graphics (after all, it is not an old software and an old technology).
The OmeletGuy's wishes 5th seems to be compatible with the actual technology (use other partition to save snapshots) but I'm not sure the 6th will be possible (specially that you can't have part of the drive encrypted, for instance...).
Because of this, maybe the integration with CB could be possible (redirecting the snapshots like "backup").
About KoPRoSKyLo's 3rd wish, well, I see it much complicated to manage with changes belong to the system and which not. Take another snapshot, goes further. The processing and the future situation of each snapshot will be impredictable. Keep CTM simple and viable imho.