If you hold down the mouse button with auto weapon you will shoot continuously. Then you reload but if you don't release mouse button it doesn't start shooting again after reloading finishes. That for me was a major problem.
Bounce and pierce don't stack. Pierce is great for aerial units whereas bounce is great for ground units. Since they don't stack you should have the option to choose one or the other instead of being stuck with bounce 2 when you upgrade to full.