Wilkinson,
The concerns you expressed are the same frustrations many of us DX users have felt since we came to realize that the touted "native PDF support" means you can put them on the device, read them, and that's it. Frustrations aside, I love my DX and use it all the time to study. If they fixed some of your concerns and made it possible to mark/ highlight/take notes in pdfs, the DX would go from a 3.5-4 star device to a 5-hands-down-best-thing-ever star device in my mind.
Now, to answer some of your questions.
1. I have never heard of any way to change the way landscape mode starts chopping up pages into three after a couple of page turns (other than to rotate back into portrait mode to "refresh" the screen, but that could get old real fast). Someone correct me if I'm wrong.
2.
Here is a great thread on the discussion boards that talks about reformatting pdf files into other possibly more readable formats (depending on tables, columns, and other variables). Hope it helps.
3-4. Don't think I can be much help for these ones either. All I can say is you might not want to hold your breath for number four, even if people are displaying their disappointment directly to Amazon (if you've read any posts about folders, you'll understand why). However, with all these new large reading devices coming out (the Skiff and enTourage eDGe, for example) that have better pdf functionality, Amazon might feel some pressure to get things changed faster.