1. By the time a composition of mine reaches about a minute in length, I feel like I've covered all of the fresh material I can in that piece and that adding anything more would result in excessive repetition. As a result, most of my pieces are way too short for their own good.
2. I can't figure out how to consistently write counterpoint that sounds both smooth and clear. I can combine well-written melodies while following all of the rules set down by the likes of Fux and similar authors and still end up with a result that sounds poor to my ear. Part of the problem is that I'm just too picky about the resulting sound as seen from the fact that I find a significant amount of Bach's music, the work of a genius, to be excessively lacking in smoothness and clarity as well.
3. I have very little knowledge of how to mix the music I compose. I've focused on learning how to control what appears in the sheet music to the exclusion of considering the subtleties of sound levels, audio spectra, and the like. When I want a decent mix, I usually just use a program I downloaded that automates the mixing process in an imperfect but usually satisfactory fashion.