A simple options screen would suffice. Basically it would just be a menu where you choose the difficulty mode, game mode, and character you want to play as when you choose "save and run". This way, ctrl+r still takes you right into the game. The default options would be jazz + single player + normal mode (as it is now). These settings should probably be saved in jcs.ini.

As for the JJ2-specific things in my post, they are there because JCS is primarily a JJ2 level editor. Even if it is expanded to support a few other related games, it will still be used for JJ2 levels the most. Therefore, I think it's a good idea to focus on features that will be useful to the vast majority of people (leaving out features in the name of making the editor compatible with say, battery check, would be foolish). Besides that, this thread is specifically about a new JJ2 level editor.

However, there is nothing wrong with putting some very specific data (such as the radius of a steady light event) into some external file. MCE data could possibly be handled this way too, though it would have to be a bit more complicated. This way, a hypothetical JCS+ would still be able to fully serve the purposes of jj2 level editing, but it could easily be reconfigured to work with other games.

Also, if the editor supported multiple games, it should really have a different mode for each game. Opening a battery check level file would mean, for example, that the editor knows not check for JJ2-specific errors (instead it would check for battery check ones, whatever they might be). Sprites would be loaded from that game's anims file, rather than JJ2's. And so on. This way, the editor would (ideally) serve every game equally well, in whatever specific ways are needed, rather than clumsily trying to support everything at once (to the detriment of everything else).

In conclusion: I think it's possible to make an editor that supports JJ2-specific features and supports other games at the same time. But, JJ2 should be considered first, since it is always going to be the most popular game the editor is used for.