I prefer the 6 ball Rolling Thunder. It's durable and has more than enough pockets. I usually use only the top and bottom sections to carry 4 balls, but if I'm bowling at a venue I'm not familiar with, I can always take the middle section for a couple extra options.
The advantages of a 6 ball roller over two 3 ball bags are:
1) Smaller footprint in the bowling alley. Two 3 ball rollers take up twice the floor space as a single 4/6 ball bag.
2) Much easier to get in and out of your car. If you use a 3 ball roller, you have to lift the entire thing at one time. With the 4/6 ball rollers, you can take the sections apart with almost no effort and load them individually. Much less strain on your back.
3) More storage space for the "other" bowling items, like shoes, shoe brush, etc.
The downsides(as I see it) are cost as the 4/6 ball roller will cost more than twice the two 3 ball bags and if you fly with your equipment, the 3 ball bags are the way to go.