It's got a decent multi-page table of contents with briefs of the main articles. At the beginning of each article there are links to skip to the next article, jump to a sections list, or back to the articles list (TOC). There is usually (but not always) a main picture for each major article, but unlike the Sony reader, you can't zoom/blow it up. The articles are pretty complete and last Sunday's paper included EVERYTHING, took me like 2 hours to read it (cause I was bored, ok). So what you miss out are on most pictures, all ads, etc. Sometimes it is weird reading an article that says "as shown on left of picture...", but overall it is a pretty good NYT experience, considering. Because of the limited pictures though, I find it better than the Washington Post, which includes NO pictures.
BTW, I dunno when it downloads, but it is already there when I get up at 5 am.
Now I also noticed, that they are also providing a Blog of the NYT RSS feed for mid-day updates for $1.99. I added that to check it out. What is surprising is that the NYT Blog is BETTER. It always has a picture per article (bigger one too), and there are real HTML hyper links within the article. It just covers major articles, but I can honestly see that at $1.99 this blog feature might start to eat into NYT sales.
Improvements that I would like to see on the NYT are:
1. A custom formatted "Front Page" image so I can get a 'glance' of what the day's paper looks like.
2. Larger/clearer pictures.
3. More pictures. If it is in the paper, I want it on my Kindle.
4. Hyperlinks (ok the Blog is spoiling me).