Unless you are masochist you should always use SSDs as your boot drive.
As for SATA 2 vs SATA 3...
My desktop has SATA 2 + Sandisk Extreme SSD and
My laptop has SATA 3 + Sandisk Extreme SSD.
The diffrence of boot times is incredible. With SATA 3 it's almost instantaneous.
Does it differ with data drives, copying files and all? You bet it does!