I agree that the onscreen keyboard adds much to the frustration, as it's default behavior mimics the problems folks have been reporting on other 4.3 devices. Most of what I've come across cites keyboard issues that many have experienced immediately after upgrading to 4.3, but that doesn't really meet the requirements of being evidence either. I suppose the only real way to know would be to grab the base android build that Sammy used and compare files.
As for compatibility issues beyond keyboard input, I can't really speak to that, as I only have a few audio devices and one gamepad. It isn't really a large enough sampling to suggest that the entire stack is hosed up. My issues have been entirely related to BT keyboards, so I'm more focused on that.
You mention conflicting software, which brings up a question. Since the BT stack would be considered part of the protected core OS, apps would require root to mess with it, wouldn't they? The six axis app being a good example, as it requires root. To hook the BT stack at a low enough level to add profiles or override existing ones for compatibility isn't something that should be possible with a user level app. I could be off base here and the reports of user apps affecting BT are an interesting coincidence, but I'm not sure I can quite see where the two cross paths. The alternative is surely more concerning, as it would imply that core OS functions in this tablet are somehow exposed to being overridden by user space apps.