While I do appreciate some of the design ideas behind ST2's approach to projects, I still believe that the project system is overall quite complex, and that the complexity isn't adding value. I'd like to offer a little constructive criticism.
The obvious comparison point is TextMate. And I know you've probably thought about this more deeply than I have, since I've only been a user, and you've actually had to do the implementation work. But look what the TextMate project system offers:
Instant "project-lite": just run 'mate .' in some directory and work with that directory's files in a new window. This is what people want at least 75% of the time. No project file at all. Note that it's easy to open as many of these windows as you want.
Next step: the ability to turn that view into a project file, by doing "save project as", under the File menu. This is where the power users get started. Once a project exists, it's easy to get back to, because "open" a folder, "open" a file, or "open" a project file in TextMate are all mapped to the same "open" in the file menu. Any number of projects can be open at a time. Simple.
Ability to set up a file & folder pattern for a project, to do filtering. Power users are now fairly happy.
With these 3 features, the system of setting up and accessing projects is simple, understandable, robust, and it pleases most folks. The "File" menu contains all the needed operations, by the way, which isn't many.
(Aside about searching: the 2 kinds of search scope in Textmate (search in file & search in project) are probably all that's really needed. I'm not sure that ST2's extra scopes ("search in open files" & "search in open folders") add value that outweighs the clutter of their presence.)
I would seriously consider adopting something much more like TextMate's project approach as a starting point, and then seeing if there are ways to improve it. (You may not find that it needs a lot of improvement, unless there is something truly new to offer, which I personally haven't seen yet.)
Having said all that: fantastic software so far and thanks for your efforts! This is turning into a great editor that could really have a huge user base.