I must say that between RDP, VNC, LogMeIn, GoToMyPC and the alternatives that I definitely prefer RDP.... RDP over VPN is great but RDP itself works just fine.

Have you considered setting up VPN (even if it's just PPTP) to the system as a backup and continuing to rely on RDP? That way after you reboot, even if RDP doesn't come up (although I work from home a couple days a week (RDP into 2 boxes on those days) and have a remote Windows server that I RDP into and I can say that I've only had a problem once... The issue turned out to be a ATI driver update)... anyways back on track... if RDP doesn't come up you can jump on the VPN and restart services, access the registry and perform any management sort of things that you desire remotely in order to restore RDP.