I think its easy to want to keep the 3D - why not keep everything and do everything? But you need to balance the cost in time and resources. Keeping the 3D capabilities I think will greatly delay the Metal/Vulkan/Low-Level-Graphics version of cocos-x. The 3D parts of cocos were always kind of an experiment anyway - there are much better 3D engines around if your game uses 3D.
You should take into consideration what percent of cocos developers are using 3D. My guess is its a very small percentage. If so how much do you delay the next version for this minority of developers.
So it depends on how many people are using Cocos for 3D games. And how much added work it will be to update the OpenGL 3D parts of Cocos.
My humble suggestion is to ditch 3D for now. Concentrate on making the best next gen 2D engine. And only when thats done consider how to add 3D in a way that makes sense for the new engine.