The Thunderbolt has a bigger screen (4.3 in) than the Bionic (4.0 in), and the Thunderbolt runs an improved version of HTC Sense, while the Bionic runs the latest version of MotoBlur. I have the sister phone to the Thunderbolt - the HTC Inspire and it came with the same HTC Sense that ships with the T-Bolt. It's not bad, not bad at all. You may grow to like it enough to keep it, rather than rooting - but I rooted my phone within a week or so and now have a custom rom installed, without Sense. Finally, the Thunderbolt ships with a 16 GB microSD card, so you have quite a bit of storage space from the inception. You could of course just get the Bionic and purchase a 16 GB SD card for it, and they're not all that expensive, but it's inclusion in the Thunderbolt is a nice touch.
-Mike