Actually, I have my USB mouse & external monitor (via VGA) connected all the time and it doesn't make any difference here. I had issues with wake on 10.8.4, 10.8.5, 10.9.0 and 10.9.1, no matter what bootloader I used (Chameleon and Clover) or whether I had any devices connected or not. I guess the key to that lies somewhere else... I linked in this thread few pages before (it's here:
#751) several links with apple community pages about this very issue happening on real macs. Apparently, the latest OSX update fixed it for most people, although there are still some left dealing with it...
If I remember correctly, "sleep fix" option in the PBI is actually just executing "sudo pmset -a hibernatemode 0" which basically makes it suspend the OS to RAM only (and thus making it faster for the laptop to sleep, since writing to RAM is quicker than writing to disk). I've been using it since always.
Regarding Clover: if I remember correctly Philip said somewhere here that Clover is being considered as the replacement for Chameleon in PBI and if you ask me... I'm all for it. Though it would require few changes in the guide...