Both the original arcade version and the console version have been patched.
The first version got up to v1.03. Its most significant balance change was removing Mature's infinite.
The console version was patched following the release of EX Kyo and Iori. EX Iori vs Benimaru had some character freezing glitch under very specific circumstances. EX Kyo's EX R.E.D. Kick would freeze opponents if they tried to command grab him at just the right moment. Never tested how easy this was to pull off.
As far as I know, Climax removed Billy's invincibility on HD activation mid-combo.
In summary, all the game-breaking stuff has been fixed (as far as I know), and Climax doesn't have any significant changes (again, as far as I know).