The first restart after an installation can be longer, as the system software has to rebuild the caches.
If I were you I'd restart it a time or two and see if it improves. If not, you could try repairing your hard drive with Disk Utility and seeing if that makes a difference.
Personally, I'm a fan of clean installs. I just replaced my hard drive with a SSD and did a clean install of ML. Just seems to save time in the long run.
Remember the thing about clean installs is they have to be clean. That means starting out with a fresh system, migrating nothing and re-installing all non-default applications. Otherwise you may just be re-introducing the problem.
I don't think it has anything to do with installing on top of, whenever I installed ML the system always seemed snappier. Also, ML introduces some new new features like Resume which will open applications that were opened after the last shutown/restart.
How much RAM do you have?
You might check what is loading at startup. For example Dropbox updates could take time. Also, what apps are loading if the "Resume" option has been checked. There can be delays while some apps like iTunes login to MAS and other such services. My startup takes ages because of Resume and I normally just sleep the computer for this reason.
Perhaps running the automation script in OnyX will clean out some crud, but note this takes ten minutes or more to run and will actually make for a slow first startup while caches re-populate.
Try starting in Safe Mode and see if the problem still occurs?
Restart holding the "shift" key.
(Expect it to take longer to start this way because it runs a directory check first.)
If this works look in System Preferences > Users & Groups > Login items and delete any third party login items (-), you can always add them back with the (+).
Also look in /Library/Startup Items. Nothing is put in that folder by default, so anything in there is yours.