A system for users to register and use plugins would be a good idea. Maybe even re-write everything but the most basic features of the engine as plugins, so users can disable them if they want.

In the new GMS 2.3 version, tby_src_runtime() holds a big switch statement for every command. Since a plugin would most likely add on to this, maybe somehow split this into different files - a potential plugin would then just register this file and a signature for calling the command in TbyChunk.