I fish a lot with a friend who has a 16ft aluminum boat with a jet motor. The river we take it on is very heavily weeded. Problem is the weeds keep getting sucked into the water intake so we have to stop and pull them out.

Is there anything that can be done to reduce the number of times we have to clean weeds out?

I don't really have a solution for minimizing your problem with weeds getting stuck in the intake, however a soft wire brush or a medium to stiff plastic bristle brush is a fast way to break up the clog at the intake if you're sick of yanking it up and down and reaching over to clean it out. Just a thought. I fish a lot of really weedy lakes too, but my 115 hp Evinrude stays pretty clean. The only time I ever have a clog is if I happen to run it through really mucky areas. I always try to trim up as far as possible to avoid the problem though.

Jet drives and shallow water don't go well together. That's why you don't see them on swamp boats. Grass and debris is going to plug the intake and dirt/sandy bottoms is going to eat the drive screw and housing up very quickly. A lot of people think they are shallow water motors, they really are not, they are for waters that have a lot of obstructions just below the surface like limbs and rocks. Get them less than a couple of feet from the bottom and you have what you are getting now.