I bet your charging system isn't that bad at all. Its the cheap ass batteries they put in there. I've just replaced my second battery in three years. The minute they start loosing a little cranking power, just get rid of it.
Also, keep your bike finely tuned so it starts quickly. You only get so many stabs at the button before the battery craps out. Mine starts really easily. Be in neutral when you try to start it. A cold yamaha engine has a very, very grabby clutch that will make it difficult to turn over.
actually, I don't think there is anything wrong with my bike at all. morel of the story was that if my batery gets low, it will not charge back up at idle. In both cases I've had the failure, it was on long rocky loose down hill single track. like 2 hours down hill. durring that time the bike is mostly at idle or near idle, but because of the rocks and bolders I'll stall it often and only use a short brap to get over.