I’m a contributor to this Blender addon, which enables Blender to import/export a specialized model format for a video game. The number of custom properties needed to fully represent all the needed values is quite extensive.
The problem is when any of these custom properties are animated. For example, if an “M3 Particle” is added to the scene, performance will be OK, but if a keyframe is then added to any of its animatable properties, than the performance takes a very noticeable hit, particularly the UI will refresh very slowly, which makes working with these custom properties rather frustrating.
I have a suspicion that it is somehow related to the fact all of the custom properties exist as an extension to the scene's properties, but I don't know what solution could be come to, to actually resolve this issue without fundamentally changing the manner in which the custom data is stored. It is ideal to not do that in order to maintain backwards compatibility.