I do agree more features along these lines would be very helpful! I think I have one of the further-along RPG's in C2, so I'll comment on some things I've done in regards to come of your points:
RPG (à la RPG maker)
✓ Dialogues can be easily tied to NPCs via the use of families, and downloaded individually
Right. I didn't want too many external calls, so I do it through events, but I simply have an instance variable on the invisible rectangle I use for each NPC. Then I just have sub-events for each one. Pretty simple, easy to follow, allows for them to say different things depending on game state. Maybe not as elegant as what others may do, but it looks and handles nicely and I don't have to play with strange formatting or parsing issues. It could even be simplified with functions, but I'm happy with how I'm doing it and it hasn't bothered me for the 50+ NPC's I already have in-game.
✗ Tilemap object is very deficient: can't add properties to individual tiles, no multi-tile entities, can't apply shading to single tiles, collision mapping must be done with separate object, tile placement is cumbersome, "open-world" layouts eat lots of memory (there's no option to only load visible tiles)
For tile-based games, I'm sure this is significant. I don't use that technique to build maps, though, so I don't have these issues. I have a lot of tiled backgrounds and sprites that I use (and re-use in different ways) as overlapping building blocks. That way, I can get a lot of customization, I'm not tied to a grid, and performance doesn't seem to be an issue even on my older desktop.
✗ Can't do isometric (yes I know you technically "can", but there's a lot of pain with back-to-front rendering and z-ordering for pseudo-3d complicates matters further)
It's a pain. It works for me, but there are still minor tweaks that always need to be done. This is particularly cumbersome with Sprite files because any global z-ordering shenanigans will re-order the body parts (and then I have to re-order them correctly after each z-ordering pass). This could be better, but I do have it working fine. I have a layer where things can be sorted and then layers above and below that are static. This reduces the amount of objects being ordered quite a bit.
✗ NPC movements (i.e. wandering, chasing, fleeing) must be coded by hand (a behavior that attempts to do this would have to tie into c2's tile structure, generating a dependency that the SDK doesn't tell us how to address)
Also a pain. I just have to do it manually. There are a few good ways to do it (the best, to me, being to set waypoints and have characters move towards that then advance to the next).
✗ Inventory is hard to manage, requiring separate projects and, in some cases, even plugins
I don't have this problem. Granted, I do limit the number of inventory objects in the game. I have 6 always-there item types (money, potions, etc) and then 4 slots for quest-related objects. The code for the 6 is easy--just pull numbers from an array and update the UI with those values. The 4 slots are a little tougher since I need to have imaginary holding slots and such for letting the user place objects and such. I just have cross-reference array values and then set the visuals to match based on what values are in those slots. It's complicated, but works flawlessly.
✗ Windowed interfaces are hard, little can be shared and there's no concept of "sub-layouts" to ease this. 9-patch object sometimes shows seams, hardcoded interfaces are tough to reskin, sub-components (sliders, checkboxes, accordions) are hard to reuse since "widgets" don't exist
I just have the UI set up on a layout how I want it, I wrote down where everything needed to be (relative to the window since I support multiple resolutions) and just create the objects at the start of each layout like that. Then, to change it, I just have to change that create call. Now, setting up that create event the first time is obnoxious, but it's the best solution I can think of. I'd love for something better, but this seems best to me.
Good list! I hope it leads to more features!