I find the program really useful and can forgive its little quirks.
I would welcome customisable keyboard short-cuts, and in Control Panel it would be nice to have more of the settings remembered between program invocations.
As for making it more Windows-like, fine providing existing functions don't get compromised. I believe in function being far more important than form and would hate to see the program dumbed down, or its operation slowed down, just to make the interface pretty.
For those with less than 20-20 vision, a wider choice of icon sizes would be helpful.
A global (as well as individual) setting for scalable symbol font size would be handy.
I agree the Help manual could do with revision/expansion, e.g by providing some numerical examples of circuit element syntax. Help is there, but it's somewhat cryptic.