I don't frequently use either - I'm a pen tool guy. (which may explain my lack of knowledge in them), but what is the actual functional difference between them?
Not a whole lot other than the brush automatically applying a brush appearance.
You can't use the Brush Tool unless you first choose a brush to apply to the path.
You can't apply a brush appearance to a Pencil Tool path until after it's been drawn.
I can't remember exactly, but I believe the Brush tool came first. Then Adobe merely removed the auto-brush application and there's the Pencil Tool. Other than this functionality, there's really no difference. In fact, double-click them in the tool bar... same options.
Adobe often does this to make it seem as if there's some new feature, when really it's only a different presentation for existing functionality options. I.E.:
- The Blob Brush Tool - Just a Brush with a calligraphic appearance set then expanded.
- The Bounding Box - Just the Free Transform tool with a few options removed.
- The Scissor Tool - Just the Knife Tool with only a click rather than a drag
- The Shape Builder Tool - Just Pathfinder operations
It's these features that may make working faster or easier, but they don't offer anything unique in themselves.