[Galaxy S II Android Development] psychlist:
First, if i've understood you correctly, google+ and wi-fi are no longer keeping your phone awake since you flashed 4.6? If that's true, then you can forget about them. If you get a problem with either of them again, that's the time to think about them.

Second, it sounds as though your media scanner is not working properly: it's probably keeping your phone awake trying to scan your media, and evidently not being very successful at scanning (hence, no pictures or videos showing). You can read a lot about media scanner problems in this thread and in other xda threads. But whatever you read, bear in mind that android's media scanner has been problematic since ics, and problems occur with many roms, custom and stock both. Google, with all its resources, has so far failed to cure this problem, so probably the best you can hope for until they do is a workaround. So probably the short answer to your question Why? is Because android media scanner is crap.

I'll tell you how i've dealt with such problems, but bear in mind that other people will have come up with other ways of dealing with them, and probably some of those ways will suit you better, so it would be to your benefit to search on xda.

In your situation (and i have been in your situation), i would reflash the rom, then check whether media scanner was scanning all my media, and then allowing the phone to sleep once it had finished. I would also check whether any other app or service was keeping my phone awake when it should be asleep. If anything was not ok, i'd flash again (and again and again ...) until i had an install that was ok. Then i'd take a nandroid backup. Then i'd begin adjusting settings to my liking, installing apps etc, checking regularly for problems. If i got problems, for example after installing a certain app, i'd probably try clearing the app's data, force stop the app, uninstall it, then reinstall it, then check whether the problem was still there. If there were still problems after installing it for the second time, whether i'd try for a third, fourth etc time would depend on how much i liked the app (because the easiest option is simply to do without that app). If i felt i couldn't live without the app, i might try (i) restoring the nandroid backup and installing the app straight after that to see if there were problems then, or (ii) reflashing (full wipe) the rom and installing the app straight away to see if there were problems in that situation; but i've never been in that situation. Once i had everything set up to my liking and working ok (no unwanted wakelocks, media scanner scanning properly etc), i would take another nandroid backup. I would also periodically take nandroid backups as i went along installing new apps (an addiction i have) and tweaking settings (another addiction). If at some point i encountered problems, for example unwanted wakelocks, i would simply restore the last nandroid backup i made when there weren't any problems, and start over from there. I would also regularly back up apps (e.g. using OBackup or Titanium), so that i could easily reinstall any apps that weren't installed when i last made a nandroid backup - but one at a time, checking after reinstalling each app whether that was what caused the problem.

You will see from this that i don't concern myself with the question Why? so much as with the question How can i fix this? The answer to the Why? question might tell you how to fix it, but you can get an answer to the How can i fix this? question without needing an answer to the Why? question.

I'm a big fan of reflashing and of nandroid backups, because so far i've found that i can cure almost every phone problem with one or other of them.