Q: Can I ever play as a boss character?
A: Short answer: not a chance.
Long answer: not a chance in hell.
Too long to read answer: No, not a chance in hell. First of all you need to understand the mechanics of this game.
The only reason we aren't able to play as Super Sonic is because Super Sonic isn't a separate character, it's part of Sonic. While this isn't exactly true, the Super Sonic file is separate from the other Sonic files, Super Sonic doesn't have any references on the disc other than on Sonic himself. So in order to play as Super Sonic, you'll need to load Sonic first.
To a certain extent this also goes for the boss characters. In fact, the linkage goes beyond that of just requiring one file for the boss data. These characters are part of the stage itself. They're comparable to stage hazards. They are linked to their own stages.
Now they still are separated from the main stage file to a certain extent. Let me explain it this way.
Let's say that the stage files are packs of Big Red chewing gums. There are about five Big Red gums in one package, and to keep them from melting to each other or the main package, they're wrapped in wrapping.
Each gum represents part of the stage data, so let's say one gum is the actual stage while the other one is the boss character. Now let's say that there are just two types of gum, the gums in the golden wrapping (the boss characters) and the gums in the regular wrapping. On the golden wrapping is a code, but it must be decoded by the instructions in the regular wrapping.
So, basically you'll first have to unpack the Big Red chewing gum pack, then you'll have to unwrap a regular wrapping to read the instructions, then you'll need to unwrap the golden wrapping to read the code. Sure you can try to read the code on the golden wrapping without the instructions, but you'll just fail with that. You need the instructions.
And that's the same with boss data. In fact, it's even the same with the regular stage data, only difference is that we always read the stage data, so we won't really notice that there is a step in-between.
Basically you'll need to load up a stage in order to load up the boss character. Since it would then limit us to only get to play them on their stage, any code would probably not be worth it.
However, another problem is the fact that they are coded differently. They all seem to have more or less moves than regular characters. In fact, their moves aren't mapped. You can't even control them.
So, no, you will not be able to play as boss characters ever.
