Well, from what I can see, you can't load a single file from an asset bundle without loading the entire thing which is pretty wasteful. Seems like a pretty big flaw with asset bundles
I would say that's a pro for asset bundles, not a con. It allows Unity to organize the bundle's contents sequentially, dramatically decreasing load time (on HDDs) for assets that are often loaded together. You just need to be aware of it and don't use bundles for things they're not meant for.
but then, I don't use Unity, and I'm not really familiar with bundles. I'm only speaking on what it sounds like to me.