This is the same problem that happened when FAT32 was introduced.
So you put Win95 or DOS on a smaller 16Bit partition, and formatted the rest to 32.
Similarly Windows 7 will not let you boot from exFAT (I bet this will change, but it would be v2). It was only intended for external drives.
Short-sighted as ever, not thinking about when solid-state is standard !
I should point out that no matter how fast the potential speed of whatever USB stick you use, you will be limited by the speed of the USB port, and also lacking DMA transfers will hammer the CPU with interrupts, thereby slowing everything during heavy file accessing.
I always partition my drives, and format depending on their usage.
Windows has a lot of small files in it. Data partitions tend to have larger files.
I always make a dedicated partition for TEMP data (ideal on a 2nd drive).
Here is a common setup I install on customers PCs;
C: System / Windows
D: Programs (and games)
E: DATA (Documents folder)
F: TEMP
If you point all Temp output to a separate partition, you will massively reduce the fragmentation of windows, and reduce the main wear on the drive to one partition (which is easier to map-out).
Things to redirect like;
Swap file, Widows temp, User temp, Internet browser temp, WinRAR/ZIP/ACE..etc, video/audio creation/conversion progs, streaming media progs and browser plugins, Steam, and anything that doesn't clean up after itself!
This also gives a little more security, as any potential malware threat will arrive in a partition you don't mind immediately quick formatting
If Windows becomes irreparable, again you can pretty much get away with a quick format and re-install.
Games and game-saves safe in D: and music and videos safe in E:
You can disable indexing on the drives that do not contain your documents folder (or switch the service off completely).
It is also worthwhile switching off "System Restore" for drives you do not need monitoring.
The boot drive is the only important one. This will save space and reduce disk usage.
On drives containing lots of large data files, it can be worth over-riding Windows default block/cluster size during format.
Larger blocks equals faster sustained transfer rates, as the PC has to ask for data less often.
Another benefit is less space is required to keep track of the contents of the partition, so leaving more for you to use.
