I've had that idea some time ago as well. I think I've read somewhere that the usb2serial firmware barely fits into the currently used usb chip. To still have the use of a 5V serial port, the firmware would either have to be switchable (jumper/switch) between ISP and serial mode OR implement something like the pololu programmer, which provides 2 serial ports over just one usb cable. One fakes an ISP programmer, the other one goes directly to the main chip. That would require a bigger chip (more flash). I think the additional cost would be insignificant, but would maybe eat up the price difference to the previously used FTDI chip.
The HUGE advantage of having in internal ISP is getting rid of the auto-reset problems. Quite frankly I'm sick and tired of reading posts like "upload doesn't work" and nobody deserves to suffer from that EVIL.
However, years ago I was complaining about the lack of a jumper/switch to disable auto-reset. Only a solder-bridge was added to the newer boards back then, supposedly a jumper would have 'confused' users. So I'm skeptical if we'll see this change happen in the official boards. Maybe the folks at SeeedStudio will make it happen.