I personally like the idea of having nothing but USB/Firewire/etc type ports... but I still use the old serial/parallel/PS/2 ports. As long as we still have a floppy controller on the mobo, we still have an ISA bus, and therefore might as well keep the "legacy" ports.
My main problem with lots of "legacy-free" ports on the back of my machine is that means there will be lots of cables. I would rather there be fewer ports on the board, but packaged with the mobo a hub or two. That way I can put the hub close to all my devices, and keep the cables down. The only time you need one device per cable is when you have bandwidth hungry devices... and I still think those are better left on the ATA bus. The exception to this are portable burners, which are pretty slick. Other than that, pretty much everything else could be on one port, especially if it's USB 2.0.
My solution to all of this is to have a machine that I have all of those "legacy" ports on. 5.25" floppy, serialx4, parallelx2, IrDA, etc. This machine is my server, and gets all the hand-me-downs from my gaming machine. The system works quite well, and once stuff is upgraded in this older machine, it isn't worth much anyway.
So, let's go "legacy-free", but be smart about it. 50 USB ports doesn't help things when the grand majority of us only have 5(?) USB devices or so, and probably a hub as well.