Thirsk, just to share my experience, I too rarely have base defense missions even with though I play with aggressive retaliation on. I don't know why this is because others say they have them often, but I get maybe one in an entire campaign.
Just to test, if I just let time run without shooting down any of the UFOs I detect, I'll get a base defense mission fairly quickly. But if I play the game through properly and shoot down every UFO I detect, then I almost never get base defense missions. I agree with you that they're fun and a change of pace from the regular crash site missions, so I wish I got them more often.
Asking a follow-up question, is it "moddable" to change the chance (as a % I assume) of the aliens detecting your base when flying by? I assume this is hard-coded because I haven't seen it in the rulesets, but asking in case.