Yeah, I think almost anything covering the intake has the potential to get clogged
Maybe you can just do it on the upper part, and leave the intake as it is, so that you can periodically take off the covering and rinse it out. As the ferns grow in, they will probably cover the opening in shadows, so once it's darked with biofilm and such, it probably won't really be noticeable.
I think that is a good idea! I can leave the filter material... its gotten quite dark around the water intake anyway!
As far as the plants are concerned, is it ok to have java fern under a fairly strong current? The water would pretty much be dumping down on them the whole time... in my mind it will look like plants being pushed down by the water of a stream.
I want to do this project in the next few days so I will for sure post pictures!