In fact we had endless discussions about this - knowing this should be hardware dependend.. Now MP just gives Windows more time to re-init the USB devices before we hook up the remote again.
Of course this will be in stable 0.2.0.5 when it arrives ;-)
I'm having the same problem with MCE remote when waking up the htpc from S3and obviously it seems to be possible to solve this. Unfortunately I'm not enough nerd to work with the svn stuff.
I guess I have to wait for the 0.2.0.5 but could you give me some hope by telling this will be available some day.