I agree with all of this. I also think the interface could be improved in a way that adds a lot of functionality to JCS, though:

There are a number of things which you can do with j2l files that can only be achieved via external programs, such as reworder.exe. Having tools like this available in JCS itself would be convenient (some sort of low level tile cache editor). Saving the level should NOT reset the tile cache, unless it absolutely has to (or you tell it to). No more rwmacro stuff.

A better editor for text strings would be nice. Reworder.exe also contains this. However, I would also like to be able to colour text strings without having to type ||||||| after each letter (just have the program add them automatically and hide them from the user). Text should be displayed in colour within the editor itself.

There's also some weird stuff like editing the speed of layer 4 (this only makes a level look weird, which is why it's locked in JCS, but it's still possible to hack a j2l file this way). Basically, I don't think the editor should lock away things like this, even if there isn't much use to it.

Further customization of jcs.ini would be good. Right now you can move events around and rename them, but you can't change the structure of the event tree itself. For example, there will always be an "enemies" tree with "bad guys" and "end bosses" categories, currently.

I'd like to see improved tools for placing tiles within a level. This includes simple things like flood fill and line drawing, and more complex things like being able to lay down certain patterns of tiles. That last one would be hard to make, though.

The edit window should display more information. There should be a toggle which switches between displaying events as JCS does now, and displaying them as sprites. For things like sucker tubes, which don't have sprites, extra information can still be given (for example, an arrow pointing in the direction the tube goes). Springs could have a line extending from them which shows how high they take you. Lighting events should have a circle around them which shows how far they extend. That sort of thing.

There should be a way of keeping track of warps and trigger zones. A good start would be able to search for say, warp target #50, or display all warp targets, or that sort of thing. Perhaps some sort of labeling system could also be helpful - you can name trigger 10 "door trigger" so you always know what it is (though I'm not sure how easily you can save that in a j2l file).

An MCE editor would simplify things a lot, especially for more complex MCEs (ie anything involving more than 3 events). What you would do is tell the editor to place an MCE at a certain spot, fill in all the info, and then the editor would put down all of the necessary stuff so your MCE works the way you want it to. Then you can have easy regenerating trigger crates.

When placing an ambient sound effect, the editor should give you a list of all the sound IDs that actually work, and allow you to preview them.

I'd like to see some kind of error checking. This would scan the level for things like warp targets placed to the right of solid tiles (these get you stuck), missing warp targets, flipped scenery tiles which will cause access violations, missing start positions (crashes MP levels), scenery events placed on non-animated tiles, and so on.

Finally, "save and run" should be a little more advanced: I want to easily be able to play as spaz or lori, choose the difficulty mode, test in modes other than single player, and so on, right out of JCS.