Personally I don't know that I like the idea of scheduled WPVP... The random element has been a key element of what makes it fun for me. Might as well just que AVs if horde and alliance are to schedule play dates. Atleast numbers should then be more or less even, even if it would solve some of the issues you've outlined.
The incentive, disincentive structure I feel is the most natural way of increasing willingness to defend (even if it does not necessarily address the issues brought by low populations). Maybe add a weekly, or even a daily quest for X amount of HKs on enemy players within a friendly capitol city with worth while rewards. I'm suggesting daily for the simple reason that it would be less likely for people go think "I've already done my quest this week, not worth it anymore".
I'm not really sure what the correct solution here would be, and I don't know if it even is possible to work around the key issue of population without solutions like buffing guards and bosses to a degree where smaller defense forces have a chance of causing enough disruption, which then lead to more issues when the defenders can actually muster good numbers.
From the horde side I can say that there are seemingly rarely groups formed solely for city raids (from what I've seen anyways), and it's more of a case of "we're already grouped because we did X, so we might as well go pop in", which is why it appears to occur at odd hours as well.