It's true that for some, the WP template can be challenging, but I would not characterise it as being the worst template system out there, and believe me, I've used a few.
There is always room for improvement, and constructive comments and suggestions are always welcome. I don't think that there are actually a zillion CSS properties in the template; the number is probably far less. One thing that WP does allow, is that with that CSS, you can do one of two things: leave it as is, and let the default property values style you page, or, use the properties to have total control over your page. It's actually the best of both worlds, since you can do as much or as little as you like.
What are your suggestions for making the index.php file less confusing? What specific things do you see as being part of a better template system? My version of a good system is likely different from every other user in the WP community. I'd sure be interested in hearing your ideas.
Thanks for posting. If you have any questions about any part of WP, don't hesitate to ask!