Might be worth reading....
http://dbmail.org/dokuwiki/doku.php?id=mysql_notes
http://www.mail-archive.com/dbmail@dbmail.org/msg13165.html
For general web server use innodb_file_per_table seems pretty sensible.
On a windows file system unless it was contained on its own partition autoextend would cause a lot of havok like the default page file setting( windows writes to the first available space for write speed hence the fragmentation issues ). I can see how one file can be an advantage but Linux file systems are usually pretty organised and seperated. On the other side if I was a DBAdmin seperate from development I might set a large fixed table space size so any future infractions may be guarded against by the code monkeys turning the server into a secret movie sharing service. There is always a minor war between DB Admins/Developers/Network Admins. Doing all three well a degree of schizoid personality is helpful, a lot of things are done due to the belief in Murphy's law and not wanting to get a phone call on a Sunday.
Depending on the file space on the server and customisation options, having a seperate partition for the database probably negates any future issues with either type. An ibdata file is a virtual partition so being contained in a real partition will cause less infractions switching to innodb_file_per_table later or vice versa. I hate doing partion sizes, too committal 😉
Data size 2GB, is that the dump or the actual space consumed? With databases that large it is also down to other things like the reduction of things that cause temp table creation( group bys etc ) as that process can turn bestial and just eat everything, RAM and hard disk access. If that is the dump you may be suprised that the database is a multitude bigger.
Also depends if you are running a public high traffic site or something else. Lots of variables to consider, but whatever I said I hope it has been helpful 🙂
