I pretty much agree with blur's focus on multiplayer, even though I personally would love to see enhancements to SP, and I am more interested in SP than MP. The thing is, any specific addition to JJ2+ is going to see a lot more mileage if it is multiplayer focused. With single player, he basically has to add new features and then hope they get used in levels. Therefore, efforts in this area are better put into bug fixes (the suggestion regarding hurt events and fixing bonus levels is a good example), and features that just happen to work in SP anyway (like death pits).

For a truly useful expansion of single player, the I think the person making the levels should be the one who controls what new features go in. One way to do this would be to mod the game itself, or create a "utility" like what karrotshire has. The latter is a bit easier but less powerful (it's basically just editing memory addresses).

Even better would be a scripting language that allows you to modify game variables and call functions, and I understand something like that is/was being worked on. Though I'm not sure how far along it's come or if there's even plan for a release. In any case it's been attempted before, and if something like that was ever made available, it would be FAR more useful than anything JJ2+ could do. It would allow you to write scripts that do whatever you want for levels, instead of having to write and compile new programs. And if the scripting language was designed properly, you could do crazy stuff like have a level with 20 exits and make it so triggers you activate in one level are carried over to another, to name just two of many possibilities.