Here's my wishlist (well things I didn't see in the lists above, but I'm lazy and didn't look so hard either.)
1) In-game script editing - at least the point and click stuff (place an npc & add dialog, place a door that works)
1A) Also, just a rant. The point of using a scripting language instead of a compiled language is that you don't have to compile it, it's interpreted on the fly. You should just catch the errors if the end user makes a mistake (there are several ways you could go about this, saving states before running the script if you're in a debug mode would be nice). I should be able to modify scripts while the game is running (If not, let's just use a compiled language - and get compile errors instead of program crashes).
1

Intellisense - Anyone who's programmed with a modern API probably likes the auto-completion/suggestion behavior of current clients. If you have to do any scripting (and it seems like there are quite a few scripts out there), then this just makes the process easier.
2) In game tile editing. It's a bit rough that I have to exit my fullscreen game, then look at the tiny images on my TV (Probably in the minority here for using the largest monitor possible). If I could edit maps in game, I would have an easier time seeing what I'm doing. Alternatively allowing a closer zoom in the editor for maps could solve my issue.
3) Graphic editing support - This would be a nice thing to have. I've used paint, paint.net and gimp for editing graphics so far, but I don't think any of them are well-tuned for pixel art (They're definitely usable for this purpose, but I feel that there could be something better - being able to pull up an editor on a running game and see graphics update in context would probably be pretty powerful). This probably won't help me anyway, but maybe someone with artistic skill would appreciate it.
4) Better music support - I was surprised that I couldn't import midi files. It seems that they can be added by being placed in a directory. It's strange that there must be strange steps to import midi files, when that's probably going to be the most popular way to compose music for the non-professional artist.
5) Additional features - It seems like it's really hard to make the program use a weapon/armor, or to equip them during battle. You could definitely use weapons/armor in FF and DW games, so it's surprising. It was a real pain to make equipping items work, probably items were overclassed (could have just had a type variable instead and kept them all uniform and generally interchangeable). There are workarounds (like having skills assigned for equipment), but there not exactly the same as old school RPGs that you might want to imitate.
I haven't messed around with this for very long yet; If there are good solutions for these things, let me know. I like getting things on my wishlist.