Certainly, but as you say it's a bit harder.
> does it make up for the general complications with using quats?
I'm sure that's context dependent, and don't have much of an opinion which way it's likely to break in general. I was just throwing something in the "pro" column that hadn't yet been discussed.
But composing, interpolating, exponentiating, etc. is a lot nicer with quaternions. (Easier to reason about, numerically better behaved, computationally cheaper.)
If you need to apply the same rotation to a large number of separate vectors, keep your rotation representation as a quaternion internally and convert to a matrix just before vector rotation.
Also, it is not really interesting what matrices or quaternions "can do". What is interesting is what we can do with them. And quaternions make a lot of things possible that are intractable or at least a huge pain with matrices.
Yes, that was my point, that what you can do with quats is a strict subset of what you can do with 4x4 mats. Not sure what you thought I meant.
> quaternions make a lot of things possible that are intractable
Such as?