I've found plugins to be extremely hit-and-miss, though.
I was helping a photographer friend who bought a commercial theme, which broke admin-side Javascript when he did the 3.4 -> 3.5.1 update. We still haven't figured out exactly what happened, but it just reinforced for me again that a) Wordpress hasn't adequately documented which APIs are stable and not, b) Authors, even of paid add-ons, don't keep their stuff up to date.
The theme replaced jQuery bundled with WordPress with some external version (eg. Google hosted or otherwise) and did it so on both the admin and front end. That's usually the cause of those sort of issues. 3.4 -> 3.5 brought up a lot of JS compatibility.
Look in the theme's directory for `wp_deregister_script` and see if anything was deregistered and re-registered (`wp_register_script`).
> Wordpress hasn't adequately documented which APIs are stable and not
If it's it in a major release, it's stable. When you buy any piece of software you're relying on its author knowing "the right thing to do (tm)". The author of the commercial theme thought it was okay to replace some bit of core javascript and din't bother to check on it. Or they didn't bother to be specific about it -- only do custom JS stuff on their theme's options page or on the front end. It's easy to do that, but you have to know how to do it (it's not documented in the Codex).
I was helping a photographer friend who bought a commercial theme, which broke admin-side Javascript when he did the 3.4 -> 3.5.1 update. We still haven't figured out exactly what happened, but it just reinforced for me again that a) Wordpress hasn't adequately documented which APIs are stable and not, b) Authors, even of paid add-ons, don't keep their stuff up to date.