I have got the stock panniers. They are quite pricey, but I got the bike fully optioned for a good price.
The stock panniers are quite small (17L IIRC), especially because they are narrower in the middle. They are made of hard sturdy plastic and handle shocks well. However, they do vibrate quite a bit. I like the fact that I only need one key to operate the bike and access the panniers. I think that's the main advantage.
Depends on your needs. The 300 is a decent bike. If you do a lot of highway commuting it may be better to go with a 650. The 300 has a very high-revving engine, which can get tiring on longer trips. I don't have a problem with it, the engine is very smooth nonetheless.
The seat is definitely much better on the 650 and the 1000. The seat on the 300 is like concrete. As a consequence, I ride a lot standing up.
the greatest feature of the OEM side boxes is their size. the size is proportional to the size of the bike, they don't stick out of your handelbar width so you can manuver through teraffic with more certitude that you are not hitting cars or sliding the boxes on other cars. If you travel solo and you don't tour around the world, I'd say these boxes are pretty suitable.