If TB is that fast, then why haven't they replaced the SATAII/III connections with internal TB connections?
Because no single drive could reach the maximum throughput of ThunderBolt right now...
TB is a link to PCIe, in the workstation market there are a few PCIe SSD cards that offer ultra high performance but those speed aren't useful for a personal computer, even less in an all-in-one computer.
The fact is the only way to fully use TB bandwidth right now is to have a fast RAID box connected to it, and that almost goes too for USB3.
A lot of single USB3 hard disk offered right now (1 Gbit/s) will just never reach the maximum transfer rate of the bus (5 Gbit/s), and the same goes for SATA buses (3 Gb/s or 6 Gb/s). The only way for a single drive to reach the max is to be a VERY fast SSD (whose controller emulate stripping sending bits of data to multiple memory chips to reach those speeds).
So from a technological standpoint if you have a USB2 port and connect a USB3 hard disk on it you will be using the drive at 40% of its capacity, and regret not having USB3.
But if you really want to have the maximum performance of 5 Gb/s out of a hard disk system you would need a RAID system anyway and in that case why on earth would you want to have a RAID system on an inferior bus with an inferior controller technology?
The way I see it USB is going to remain used and useful as a small device connector (mouse, printers, phones etc. small flash memory keys where USB3 willbe missed for a year yes) but if you want performance and reliability for data transfer ThunderBolt is the way to go, I'm eagerly awaiting to see the RAID thunderbolt offering which could lead to max performance safe data systems.
Imagine this : booting from an external TB RAID5 enclosure with the maximum 10Gb/s data transfer rate, not even internal SSD are capable of this rates!