Well, 80% of the population uses IE as their browser, but that doesn't necessarily mean it's the best solution or that there aren't a lot of problems with it... Also, you can still use IE 4, but that doesn't mean you should and it doesn't mean you're going to get support for it either from the manufacturer when you run into problems.... I'm just restating what the core team is stating about Solpart. At one time, it was by far the best choice and only choice. Those 80% of skins, some including my own, may need to have their menus converted to DNN Nav at some point in order to work or function properly. Some designers are most likely using their own "templates" to crank out all kinds of cookie-cutter "premanufactured" skins as quickly as possible and haven't taken the time to update or follow what's happening with DNN's development to follow the core team's recommendations and forewarnings. I try to follow and keep up, and don't do cookie-cutter designs, I try to keep things unique and spend a lot of careful time on the design which is just another way of doing things.
As far as the skin goes, there are differences in the menu's css, and alignment of the menu can be tricky say if you want it centered or right aligned (one of the "lost" functions), but otherwise there are no differences in how the rest of the skin is put together. It's just a matter of which menu code or token or object code you are going to insert into the menu area. To be honest, the menu is probably the hardest part of skinning. For learning, I'd definitely play with a menu setup like the Minimal Extropy menu that works and adjust the css as necessary to make sure you are overriding the defaults in default.css from the portal directory.
Also, there are third party menu modules that sell enterprise or developer licenses, they are reportedly easier to set up, true css only menus, and can be used as skin objects which could in theory be a part of the skin's install package so it could be installed with the skin as long as the license allows for that. You'd have to check with each developer to clarify the redistribution rights granted in the EULA's.