I've recently hit an error caused by an NBT tag exceeding 2 MB
Although that case was unrelated, I would hope to help prevent cases such as that

I'm currently writing a program to make drones (controlled by remotes) build a large, complicated bridge, one step at a time
This program may contain thousands of puzzle pieces, so I worry about the NBT size of the drone programs and remote
(image showing NBT data of a very simple remote GUI)

Would it be possible to transfer the configurations of remotes, along with drone programs, away from the item NBT, and instead to the world file, similar to how Maps and ComputerCraft Computers work?

This is a good idea, but probably unlikely to make into the 1.12.2 version, mainly due to time constraints, and the potential for destabilisation; it's a fundamental change to how drones store their programs, and a lot of functionality would be needed for server->client sync, data integrity verification, etc.

However, I'll consider it for 1.14.x.

Something else to do here is more compact storage; could be as simple as using shorter key names (e.g. enabling -> e, width -> w etc.) or more complex; storing in a packed binary format, or compressed JSON.