The thing that really bugs me with SQLite3 is the inability to modify tables. It's not much of a problem unless you have foreign key constraints and then it's a nightmare. Ultimately I resorted to just recreating the entire database from a script every time I had to make a change. If this is "fixed" in SQLite4 then I'm sold.
I'm surprised that there aren't any real binary integers stored anymore but I can see how that would reduce complexity compared to how numbers were handled in SQLite3.