I use math a lot in lyx, and it would seem simpler to me to combine the math toolbar and the math panel into a single, double-decker toolbar. I find myself using the panel as much as the toolbar, and I am not sure why they are separated.
One minor problem: When adding math to the end of a file, the automatic popup of the toolbar (which I like very much) partially covers the math box until one starts typing math. If the math panel is also activated, it completely covers the box. The box pops into view as soon as one types some math, but it is a little disconcerting initially. This all refers to lyx 1.6.1. Dave Raymond