• Test level in multiplayer mode
• Helpful warnings when user tries to save. Things like "Level does not contain proper start positions", "Warp on tile x,y would get player stuck", "No corresponding Warp Target for warp ID x", "Flipped animated tile at x,y could crash game", "No next level setting specified". User should be able to ignore warnings or turn off warnings entirely.
• Find-as-you-type event search, a la Google Suggest. "W"->results: Warp, Warp target, Witch etc
• Sort events list by the amount of times each event has been used
• Ability to assign events/tiles to hotkeys and to keep list of favourite event configurations
• (similar to above) Snippet library to hold personal templates (for MCEs for example)
• Ability to create tileset helpers that contain the positions of important tiles in the tileset (corners, straight platforms, slopes). With tile description for tileset in place, add paint-like tools mentioned by someone else, except these paint entire platforms using the tileset information. A diagonal line might draw a slope for example, and a block would have proper corners and side tiles. This could also be used to quickly convert levels from one uncompatible tileset to another if implemented correctly. Or form a basis for a random level generator.
• JCS for newbies #1: Event window contains links to corresponding ERE entries for each event
• JCS for newbies #2: Event window display mode where each event in the list contains an image of the event. Tuf turtle image above "Tuf Turt" event, etc. Like windows explorer thumbnail view.
• Level pack creator that finds the used music and (non-official) tilesets for each level selected and creates a zip out of it, or a file list.
• Ability to remove level password (for your *own* level) once a password has been set.
• More convenient help function. Possibly an inline help

I guess much of my suggestions are kind of enterprise-y instead of small tweaks and are useless to create if there's only a small amount of people using jcs though.