If you have a lot of meshes, implementing scene.getActiveMeshCandidates could help (see Curious about this.totalVertices.addCount() in the evaluate active mesh loop - #27 by Evgeni_Popov).
@JCPalmer has also tried something of his own, perhaps that might be of use to you?
There’s always the possibility of overloading scene._evaluateActiveMeshes with your own implementation, removing anything you don’t need.
It would also be useful to take a performance snapshot and see where most of the time is spent in the _evaluateActiveMeshes function (this function is doing mesh culling, animates skeletons, dispatch sub-meshes, etc).