I've used the Pondovac 3 in a pond with small rocks. The first time I used it, a rock blew the little vacuum slider right off the tubing. I never saw where it went. It might still be in the pond. Also rocks often jammed the valves. There is an attachment with an adustable opening, but it's still hard to clean muck out of the gravel. And if you use the algae scraper on a large rock and get too close to the gravel, you've got stone rocketing into your vac with a LOT of force.
Since I took most of the small stones out of the pond, the Pondovac is a great tool, but it's a hassle to use with a gravel bottom. OTOH, there really is no good way to clean a pond with a lot of small stones, so you might want to get rid of them anyway. Yes, they give more surface area, but with all that trapped muck, you're probably better off without the gravel anyway.
Since I took most of the small stones out of the pond, the Pondovac is a great tool, but it's a hassle to use with a gravel bottom. OTOH, there really is no good way to clean a pond with a lot of small stones, so you might want to get rid of them anyway. Yes, they give more surface area, but with all that trapped muck, you're probably better off without the gravel anyway.