The Huntingdale bus is probably worse. There was a line longer than the bus to get in the bus. A l i n e.
This only happens at peak times (At Huntingdale station, about 9-10/11, at Clayton, ~3-5?). One reason why I tend to hang around at uni longer if if I'm kept there until 3 or longer, ceebs waiting in line.

(granted, this line gets smaller as semester goes on, because less people start showing up, people start realising there's no point rushing to the bus because of the line and so might stop along the way to do something first and then get the bus, etc.)
The shuttle never gets any better, though. And is a lot less frequent than the Huntingdale bus (plus, unknowledgable JAFFYs don't realise you can take the 900 to Caulfield, 630 or the Mid-Brighton bus to get to Huntingdale/Clayton stations, and those buses tend to be very not-crowded as a result.

Me and a friend caught the 630 yesterday for this exact reason). So yeah, Huntingdale is a better option if your pushed for time, but the shuttle is better if you're not and don't get claustrophobic (because that one's FREE~)