One trick applicable to particle systems can also be used in Spine: use an image that has multiple particles on it, like maybe 3-5 or more. Depending on the effect, when animated in a cloud of overlapping particles it can be hard to tell those are all part of the same image. This allows you to get a similar effect using 1/5th the number of particles. Animating particles in Spine isn't as dynamic and is tedious, so when you do it, having less to animate is nice.
This may help with your flock of bats. Eg, use 1-3 frame-by-frame sequences, each having multiple bats, then show 5-6+ copies of those, overlapping. Of course this is a shortcut and affects fidelity, so whether it is acceptable varies.
Forcing everything to be skeletal animation isn't always best. Using frame-by-frame sequences is not necessarily a bad thing. Before Spine generally everything was sequences!
If your sequences are too large, you may be able to make them smaller or just improve the effect by mixing them with skeletal animation. Scale images to better match the next frame, so you can use fewer frames in your sequence without it looking choppy. Explosions, smoke, and similar can sometimes be done using overlapping images in Spine, with rotation and scaling (and possibly additive or other blend modes) instead of a rendered sequence of the final result. Often the bulk of each VFX can be done in Spine, often with sequences to support them. It can help a lot to have your artists be considerate of this when designing the VFX in the first place.
