The resistor would cause some small drop in posssible brightness... but would also ensure the peak voltage doesn't fry the emitter. To my mind, a sensible trade-off.
Direct Drive will drop in brightness as the cell voltages drop. Less of an issue with NiMH but a real pain with Alkaline (look at voltage discharge curves posted elsewhere on the forums and you'll see what I'm talking about). This is why I like regulated output - maintains brightness and keeps it steady until the cells can't take it. If you go regulated, you could go for all cells in series, plus have different brightness levels so you can balance the amount of light needed and battery life - keep it low and useful for long life, crank it up when you need it, that sort of thing.
There's nothing wrong with Direct Drive, it's just different, and obviously easier to build!