Well, my recent experiences of an OS X upgrade have been "interesting"
Snow Leopard on my old black MacBook (2.4 Ghz Intel Core 2 Duo/4GB RAM/500GB WD HDD)
"Nonstandard" in that I had 2 partions, one for System and one for Data (home)
SN support discontinued. Buy Lion for $20. Download (and make a copies) of the .app file.
Connect new WD 500GB HDD by USB - make single partition, install Lion, boot from new HDD, looks OK, use Migration Wizard, looks OK but still referencing Data\Home for my stuff. Copy over Home [cp -npRv "Volumes/Data/Users/andrew" "/Users/andrew"] and tell Lion that is where my stuff is. Reboot, Lion now very unhappy, can't find all sorts of stuff.
Hmm... Start again. Put new HDD in machine, start from old drive on USB, install Lion on new HDD.
Do import as part of install. Better, but Lion still using Data\Home for my stuff.
Copy Home over to Users again and tell Lion THAT is where my stuff is. Reboot.
Well, sort of OK but not really happy. Parallels has to be reinstalled because it is confused.
Repair permissions - takes yonks. Lion now want to "update" itself - huge "update" takes yonks.
Seems OK now, but Time Machine stalling/confused backing up to ReadyNAS (fine under Snow Leopard).
Hey ho - time to delete a .plist or two & see how we do.
Evidently the OS X install routines don't cater for ~\Users\yourname being somewhere else!
Mac
So not straightforward if you've split your data off from the system (which I personally think is best practice, though it is obviously better to have two separate drives)