I think it's more practical for people to make tools that complement JCS rather than replace it, anyway. Reworder is a good example. This way you can make the basic level in the editor, and do fancier things with external program. It also just so happens that these fancy things usually are rather technical, and don't have much to do with the level design (which JCS is most suited to). Honestly, I think if a JCS+ were ever made, the best improvements it could make would be interface related, such as the ability to flood-fill tiles and whatnot.

Scripting is still the best solution to the sorts of things people would like to do. A working scripting language already exists and is capable of doing some reasonably powerful stuff, but unfortunately the project seems to have stalled, as tends to happen with things like this. I imagine it could still be completed eventually, but I have no idea when or if that will happen. It's a shame really because what has been done so far shows a lot of promise, but at the moment it still lacks a handful of features that would be needed for it to be brought into practical use.