It's usually possible to boot Linux from an over-2TiB disk even in BIOS mode; you just need to be careful about partition layout so that the BIOS Boot Partition and the Linux /boot partition reside below the 2 TiB mark. Sometimes firmware bugs
throw up hurdles you must overcome, though.
EFI-mode booting is sometimes a little bit faster than BIOS-mode booting, but this depends on the firmware.
There are differences in boot loaders and boot managers between the two systems. In BIOS mode, you can choose between LILO, GRUB Legacy, and GRUB 2, with GRUB 2 being the default for Fedora 16; and there are numerous third-party (non-Linux) boot managers. In EFI mode, you can choose between ELILO, GRUB Legacy, GRUB 2, and the Linux kernel's EFI stub support for boot loaders, with rEFIt and rEFInd available as additional boot management options. Fedora uses GRUB Legacy as the default on EFI. For a single-OS system, sticking with the default usually works fine, but if you're unhappy with the boot manager or boot loader, or if you plan to dual-boot in the future, you might want to look into the options for both methods. My EFI Boot Loaders
page covers the EFI side of it.
Ultimately, my own advice for you is: If it ain't broke, don't fix it. I'm not saying you shouldn't upgrade Fedora or even re-partition for the upgrade, but if you're satisfied with the way your computer is booting now, stick with that method. Changing it just creates a variable that could turn into a multi-hour debugging session.