Back, when I did heavyweight GUI development, I went onsite for the first few customer installs and watched the customers operate the system (usually after fixing some bug LoL). Those always gave me basic UI tweaking ideas, but the real lightbulbs would come on when I asked questions like "why didn't you just do X instead of Y" or "how would you change this to make it easier". Or various other generic questions, the answers were frequently enlightening about how to tweak training materials or the UI, but I usually got one or two killer ideas that were more significant and ended up being the kinds of things later users would rave over.

So, I can't help but think you missing the most important changes if your not actually talking to the end users about what they are thinking or why they are doing particular actions that aren't always what you expect.