You can also combine a lot of options. If you have ten options, but users almost always use only three particular combinations of those options, just make one option with three choices that selects among those three behaviours.

Another good idea is to share options where possible. Find a set of apps that all have a similar option to control a similar behaviour. Make that option something centrally configured across the whole desktop. Less total options, plus as a side benefit the desktop becomes easier to configure for both novices and power users.

Yet another idea is to identify when,where, and why particular options are used. For example, many options are things that are generally only configured once. Those options don't need to be in the same place as the options users might need to change two or three times a day. (i.e., don't put "show files as icons vs list" right next to "show hidden files" - the former a user picks once for their preferred style, the later needs to be changed a lot to filter out or display hidden files.)

KDE preferences could indeed use a lot of organizational love. The organization for most of those preferences is somewhere in /dev/null. They aren't needed. They're superfluous.

The "advanced" vs "novice" user debate is an entire myth. I'm a developer; I can work magic on code in over 20 languages to do all sorts of things. Most users can't even grok the basics of how a programming language works. Clearly I'm an advanced user of development tools. On the other hand, I fire up a word processor maybe twice a month, and I barely know how to use one. And when I do, I know the parts/features of the word processor I use like the back of my hand, and the other parts are completely alien to me. How do you decide what options are advanced and which aren't? You can't make it a desktop wide choice because users are advanced or novice in individual tasks, not with their entire computer. You can't even do it per-app because, again, it depends on which tasks in that app the user is advanced with. (I can use mail in Evolution very effectively, but I don't know jack about managing group calendars, organizing tasks, etc.)

This is one reason there are so many apps that do basically the same thing. Galeon vs Epiphany? Exact same thing, yet each is appealing to a totally different set of users. That's largely a single "option" that toggles between two different application behaviours; install Epiphany or install Galeon. KDE vs GNOME? I can make them act a lot like each other, but they're still different. If you don't like one, use the other. One single option that makes a world of difference. A lot of users love Midnight Commander. Does that mean Konquerer/Nautilus should have a ton of options to act just like MC, or like some hybrid that 3 users out of ten million prefer? No, it means the users that like MC should just use MC. Users that like whichever hybrid can use the file manager that mimics that hybrid. Try to make a file manager that works for everyone, everywhere, and you end up with a bloated confusing monstrosity that works decently for very few people. Not good.