I practically grew up with the RPG Maker series, mainly RPG Maker 2000. The old ones are getting outdated and the latest ones do not offer what I am looking for, therefore I am looking for a new engine.

I want to create a top-down 2D RPG similar to the SNES-era RPGs in art style (my main influence is Seiken Densetsu 3) and with a battle system similar to Chrono Trigger's, as in the battle happens on the current map without any screen change and there are sprite animations for basic attacks, item use, and the like.

I must mention that I am a mapper first. I would need the following: support for animated map tiles. I checked out unreal engine 4 and noticed it is only possible with workarounds there, which would be rather unfeasible; the ability to make bridges, in RPG Maker I could make bridges/land bridges which one could pass under and across by creating two separate "passibility" settings for the same tile set and switching between them whenever the player character reached the appropriate areas; and the ability to switch between tile sets as a script call in-game, this could be used to make the floor of a room to disappear and be replaced by a parallax background for example.

I can make all what I have listed so far in rpg maker 2000. The battle system would require a lot of workaround however, and creating interfaces for custom menus is also horrible complicated in rpg maker 2000, but possible, since it was not made for this sort of thing. What is lacking is support for multiple operating systems. The program is also too old and I have been alerted to problems on newer operating systems, so I need a different engine. The newer rpg makers have botched the mapping with oversimplified "auto tiles" and removing layer views, so the program decides which layer to place the tile in and if you want to, for example, replace the ground under a tree, you must erase the tree - absolutely horrible.

My game would be controlled solely by the keyboard or a controller, so not the mouse. I want to make it for PC only, with multi-OS support. It would use low resolution pixel graphics (16x16 pixels a tile) and run on a low resolution, which would need to be scaled with a nearest neighbor filter applied, so as not to mess up the pixel art.

Which engine would you recommend for me? Thank you in advance.

You are mentioning so much 3d stuff: pass under a bridge, parallax, under a tree
You said you are a mapper. Why do you have such strong preferences in the art department? Anyway I always thought that rendering a video to texture can be done in any 3d engine (beginning with Build for Duke Nukem 3d).
The editor seems to be a problem. Hmm I never tried to write extensions for editors, but it can be done.

\got nothing