I'm still a bit of a noob at this, but here's a few suggestions that may be obvious but maybe you haven't tried:

1. Build churches in each province, it increases loyalty.

2. In the late stages of a game, as long as a province's loyalty is near 200% (max), you need only 100 soldiers and a small fort to prevent rebellion (barring outside mitigating forces).

3. If you have less than 200% loyalty, keep a MUCH larger force there until it hits max. I'd say at least 300 solid.

4. Spread your leader and heirs around to cover a lot of ground. Their proximity GREATLY affects happiness. I had to keep my top prince in Scotland for several years just to avoid rebellion, even though my army was vastly superior.

5. Like HRV said, don't execute rebels or their leader when you reclaim a province, it makes martyrs out of them. Release them all, lower taxes, and garrison a castle. Then after a few years, barring catastrophe, you should be okay.