I'm a pretty average build with longish arms, so I tend to be more comfortable on frames that would be considered "too big" for me according to everyone's fear of standover height. Top tube length is much more important.

The standover on my Maddy was pretty far up into my junk. I ride my bike much more than I stand over it though, so it was never an issue. If you're 5'9" the medium will most likely be perfect for you.