sqlite or mysql for large datasets
The SQLite database engine stores the entire database into a single file. This may not be very efficient for incredibly large files (SQLite's limit is 2TB, as you've found in the help). In addition, SQLite is limited to one user at a time. If your application is web based or might end up being multi-threaded (like an AsyncTask on Android), mysql is probably the way to go.
Personally, since you've done tests and mysql is faster, I'd just go with mysql. It will be more scalable going into the future and will allow you to do more.
I'm not sure what this means. When I have experimented with mysql and sqlite, it seems that mysql is faster, but I haven't constructed very rigorous speed tests.
The short short version is:
If your app needs to fit on a phone or some other embedded system, use SQLite. That's what it was designed for.
If your app might ever need more than one concurrent connection, do not use SQLite. Use PostgreSQL, MySQL with InnoDB, etc.
It seems that (in R, at least), that SQLite is awesome for ad hoc analysis. With the RSQLite or sqldf packages it is really easy to load data and get started. But for data that you'll use over and over again, it seems to me that MySQL (or SQL Server) is the way to go because it offers a lot more features in terms of modifying your database (e.g., adding or changing keys).