After 11 years of 104-key keyboards, looking at Model M's made me realize that the Windows key and appskey are a huge impediment to my being comfortable with the keyboard. They sit right where the heel of the hand should be.
I moved my AppsKey cap to the Right Windows & remapped right Windows to right alt and that's nice. I hope to do something with the left Windows key someday.
I second the idea of learning proper finger usage and then improvising. Some people find that their fingers naturally curve up toward "e" and "io," which is nice because those are common vowels.
I do NOT recommend alternative layouts: Dvorak's design is flawed (it's designed to maximize hand alternations, but I seem to make most of my mistakes coordinating opposite hands, i.e., "teh"), his research was biased (he held the patent) and faulty (no control group), and It seems that many fast typists who try to learn a new layout spend months dilligently trying to learn something new and they could never surpass their QWERTY speed. Slow typists tend to increase their speed, but I think that's due to PRACTICE, not inherent advantages of the layout. Additionally, applications are usually written with the QWERTY assumption, so shortcuts will be weird, and commands are a huge part of computing relative to typing. Finally, they're just equaling their speeds on a typing test, which does not reflects the full mental overhead of using a different layout, which will probably slow them down in real-world work.