The AI in the bonus/hidden stages of Arcade Mode are significantly trickier to beat than the same AI in versus mode on hardest. Is there a way to access this difficulty of AI in versus mode? Maybe we can move some files around in the SteamApps folders to achieve this?
The AI settings are encoded in the BCM files and are pretty much deciphered, but there isn't much room for improvement. The current 'hardest' difficulty is almost optimal within the AI framework. You can find detail in the Modding SSF4AE for PC thread. It's a long thread but worth reading if you're serious about modding the game.
The difficulty of hidden bosses is another story. It is not done by AI settings, instead, they are 'cheating' - they have entirely different move sets from the original character. It seems these special move sets are in the EXE, nobody has successfully extracted them yet. This information can also be found in the aforementioned thread.
However there are multiple attempts to recreate them based on the original version of the character, the most authentic one being Error1's boss character moveswap, you can find the download links in the video description.
The bosses are completely different characters (as NS.X. already pointed out). The problem is that they have different startup timings, invincibility etc. This might confuse you if you want to play online.
Except from just swapping files you could also change the existing character files.
The idea is simple. You use a tool to tweak the moves of the existing characters:
Or if you just want to make the game overall harder: Give your character less hit points.
I would not mess with startup and hit stun timings.