New Slide vs New Layer

When you say "instinctively, for neatness" , I would remind you not to think of what it looks like to you as you are working, but what counts is how it looks in the hands of the learner. While that is the priority, there are some mistakes you can make that will make life harder for you, without helping the learner, and you want to avoid them.

The first thing to remember is that all the layers (including the base layer) are part of the slide. Get too many objects (including triggers) on it and it gets too unwieldy to keep track of.

If there are objects that must be visible at the same time, they must go on the same slide. You can make them simultaneously visible if they are on different layers (eg. the base and/or any layer you create), but not if they are on different slides.

If you have objects that come and go, and others that come and go, etc. it can all be done on one slide, but at some point too many objects will overwhelm your ability to keep track of them, and you need a new slide. Generally, for most of us, having fewer items on a slide makes it easier to keep track of things. Layers can be one method of off-loading clutter, but sometimes a new slide is best.

If you want to add material to what is already there (and especially if you want to then return to the original) or add it momentarily, a layer is probably best. If you want to replace the material with completely new material, new slides are best.

Triggers generally can access all the objects on a slide or any of its layers, but not objects on other slide, so that is another point you may need to consider. The corollary to that is that too many triggers on one slide may impair your ability to find and modify a specific one, or on rare occasion may cause timing problems if too many are initiated by one action. I sometimes use a layer for no reason other than to hold and initiate triggers.

These are some items that aren't really negotiable. Beyond that, there is a lot of personal preference involved. If done well, the learner can't tell the difference between 100 slides, each with an object on it, and one slide with 100 objects on it.  For me, I would probably create that scenario with ten slides with ten objects each, lacking any compelling reason to do something different.

If you are thinking of bandwidth and file size, the difference there is far more dependent on the type of objects on the slide. The difference between slides and layers is nearly negligible.