The most annoying disadvantage of upgrade in place is about having old traces in the file system. Basically, each upgrade leaves old product directories, so with every step you have less and less disk space available.
Removing old files manually is not exactly safe, so many prefer advanced upgrade.
The good news is it is no longer the best option. Check Point has two scripts, for MDM and for regular installations, that should clean your system after the upgrade.
Refer to SK91060 for regular systems and to SK65330 for MDM systems. According to the SK, the latter script is already integrated into R75.50 and R76 MDM installation packages.
With these tools one can upgrade in place and still have optimal disk space available quite close to a clean installation.
Finally, Check Point!