I had lots of trouble with restoring backups when I had Titanium. I also found it complex and annoying, instead of telling me file names and junk, I just need to know what app it is and where the data for it is. Mybackup pro does exactly that. Granted it's a bit slower, but so far I have only had 3 apps have problems with it (Beautiful Widgets, which is fixed, SetCPU, this once, and Lookout Mobile Security, which I believe is fixed). Not bad considering the convenience.
I too had a program that let me link and download direct from the market, but when you get over 30 apps or so, that gets tedious and time consuming.
If you only replace roms once every couple weeks or something, that's fine, but when you flash several a week, that time adds up very fast. I have been known to flash 20 roms in a single day, and do multiple restores, so no, I'm not going to sit there for an hour clicking back and forth.
My restore method (using Mybackup Pro):
Go to settings
Setup my wireless
Set screen timeout (2 minutes)
Setup my account
Go into accessibility and set "power button ends call" (major pet peeve)
Now I start Mybackup and restore my alarms, call log and mms log.
Restore all of the apk's first minus Apps2sd and Lookout. Go grab a drink while this works.
Apps2sd creates too many interruptions and Lookout wants to scan everything, it significantly slows things down. I don't even use Apps2SD anymore.
Then go get Lookout from the market (it works this way from Mybackup, but I still get it direct)
Lastly, go back and install the app data (I manually set Setcpu, just in case)
Total time, 10 minutes, much of it waiting for the APK's to install.