There are a few features missing from Natural Docs 2.0 that were in 1.x. Some of them are temporary, some are not.
Since this is an entirely new code base, new parsers need to be written for languages to get full support. For the initial release only C# has full language support, which means Perl and ActionScript no longer do. You can use them with basic language support, or you can continue to use them with Natural Docs 1.x. I do plan to bring full support to a lot more languages over time, but these two may not be the first to get it.
Right now Natural Docs 2.0 does not support the "(see image.jpg)" syntax. It will in a future release. This feature was not deliberately removed, it just hasn't been recreated in the new version yet.
Natural Docs 1.x had a customizable Menu.txt configuration file so that you could organize the source files exactly how you wanted them and add links. This is no longer supported. The files view will now match the source code's folder structure exactly, since that's what most people wanted anyway.
Setting a project title, subtitle, copyright, and timestamp are still supported, those properties have just been moved to Project.txt. When you run 2.0 on a 1.x project for the first time it will automatically find those settings in Menu.txt and copy them to Project.txt for you.
There may be a way to include links on the home page in a future version, but it's not an immediate priority unless people tell me it should be.
Natural Docs 1.x generated various indexes so you could browse through an alphabetical list of all functions, classes, and other things. The class menu replaces the class index and everything else can be found through search.
There may be a way to create additional menus to serve as indexes in the future. I'm not sure how many people used the other indexes so how much of a priority this is depends on the feedback I get.
By default you can no longer use the keywords table, view, index, cursor, trigger, column, key, and primary key for their respective database comment types. You must use the versions prefixed by "database" or "db" such as "db table". However, if you have a lot of documentation using the unprefixed forms you can add these keywords back by editing Comments.txt. It's still possible to use them, they are just no longer the default.
This was done for consistency and to prevent confusion. Previously you could use just "index" to document a database index but you couldn't use "field" without a prefix because it's a variable keyword. If both require "database" or "db" then it's clear and consistent. Also, while some keywords like "primary key" are clearly database-related, others like "table" are more ambiguous. In fact, "table" is now a variable keyword by default. Again, you can change all of this by editing Comments.txt if you want.
Natural Docs' three panel design replaced both of them. There is no need for separate output formats anymore. Specifying html or framedhtml on the command line will give you the same result.
Topics.txt (which is now Comments.txt) had a setting called Break Lists that allowed you to document things with list topics and they would appear as separate topics in the output. That hasn't been recreated in the new version.