I agree that the Matrix blox stuff and the other products like it (aquascapes 'snorkel' and 'centipede') are the best way to go. And if all my clients had unlimited budgets, that's what I'd probably install every time. The problem is, they are all fairly expensive. And water features are already expensive. So adding these costly items to your bid can often price you out of the customer's budget, in my experience. So I get why you wouldn't want to use them. We install a LOT of pondless water features. Just finished one earlier today, actually. And I rarely use that stuff, just because of the cost.
The thing is, you do have to find a way to service your submersible pump (that is, if you are using a submersible). But irrigation valve boxes and extensions (with holes drilled in the sides) do the trick for that just fine. And they also sort of create the space you need around the pump for clean water to be around the pump - for much less than those other items cost. So we create a little bit of a void using the irrigation valve boxes and extensions. Then the rest of the basin is filled with rock.
As for the variety of rock, we always fill up the basin of the water feature with really large river rock. Like 6"-8" or larger. That creates larger voids and water can get through much easier. It also leaves more room for a greater volume of water to be stored in the basin of the water feature, which is important. You don't want to use up all the water in the basin in the falls and then run out. So there has to be enough to make it run well, and still have some water left for the pump to siphon up until the water returns. I've always found that the larger river rock worked really well for this. And I've never found it to really get clogged. We've had to clean out around the pumps, sometimes. But I've found they stay fairly clean, as long as you control algae and keep the water clear, which isn't difficult.