Regarding Gazebo RTF becoming low after increasing joints in the simulation

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Hello. I also had troubles with a low RTF with a lot of joints (actually, I think that the real issue is more the number of links/models in the world than the number of joints).

You could try to remove some unecessary collision checks (for example if you know that two given links won't collide anyway, or if a given collision is not relevant for your use case) with a collision bitmask tag, or the selfCollide tag for example. Also, try to use simple geometries for collision (such as sphere, box, cylinder) instead of meshes.

Finally, for the stability issue, you can try to add a bit of damping in the unstable joints, and enable the implicitSpringDamper tag in joints, wich is a more stable implementation of damping (see here in "<gazebo> Elements For Joints" part for implicitSpringDamper tag).