Possible sources of high CPU usage could be indexing of files (say if you have a large project open). There are also known performance problems in the latest stable release due to the underlying OS being silly that could be the culprit as well. The latest dev release has a fix, although there are still some quirks to be worked out.
User folder is always there and is where your settings are stored. Generally, package names with a lower case name are dependencies (e.g.
mdpopups) that were installed because they are required for one of your installed packages to work and packages with upper case names (e.g.
PlainTasks) are "regular" packages.
Most packages are generally going to be installed as
sublime-package files, but some (for example
PlainTasks) are installed as unpacked files in this folder instead.
Deleting a dependency is not a particularly good idea unless you know that all packages that need it are no longer installed; best case Package Control notices when you start next and puts them back, worst case it doesn't notice and things will start failing in mysterious ways.
If you want to play around with deleting packages, your best bet is to back up the entire folder so you can get back to a working state if things go pear shaped.
All that said, just because a package is installed doesn't mean that it's necessarily a CPU drain. You can select
Tools > Developer > Profile Plugins from the menu to see a list of all plugins that might do something and how much time they're spending doing things.
Using that you can see if something is spending a lot of time doing something and, if so, temporarily add that package to the list of
ignored_packages to see what the effect is. In particular, items under
on_modified are probably the biggest drains because they potentially do something every time a buffer is modified or the selection changes.