Its easy to criticise from your position but I have been maintaining and supporting this project for 5 years and have poured in my soul, time, effort, and money into it. I also created and maintained most of the 30 or so included skins so I fully understand what is involved with creating skins and maintaining skins. The skinning system is pretty good in my opinion.
There is nothing stopping you from structuring the css files of your own skins differently, you just include them in the style.config file. So if you want to make some base css files that you use in most of your skins that are the same and then put the things that are different across your skins into different css files you can. You can name them what you want and list them in style.config in the order they should be added. If that makes it easier for you to maintain your skins, great.
I started a business in the fall of 2006 to try and make a living by working full time on mojoPortal. I am not yet making a living. I'm starting to make a little money from the store but I am still burning through savings and I only can make it till the end of the year so my priority is getting to enough revenue to make a living before I go broke and have to take a job.
Ideas like revamping the skinning system or little refactorings to remove similar code are just a distraction to me at this point that will only slow me down from working on more important things that can help me reach my goals.
Hope you can understand.