If you want to programatically access bluetooth or USB drivers to transfer files you will want to go the Java route.
One thing to note is that with the Blackberry desktop manager you can configure the blackberry to use the USB connection as your network connection when plugged in.
If you want to build a simple application that can store data locally and then submit it back to a database on demand or while in coverage the VS plugin or MDS Studio work just fine.
MDS Studio and VS plugin require that you must be using a BlackBerry Enterprise server.. Java does not.
If you are familiar with Visual Studio the plugin is nice, if you are familiar with Eclipse MDS Studio is nice.
If you want some more information on the VS plugin you can check the pre-recorded webcast.. just create a login and you can view it BlackBerry Resource Center - Main