(1) Production costs
A typical custom printed stand up bag costs between 15 and 20 cents apiece. A plastic bottle costs more than double this amount. This means stand up bags have an advantage here for companies.
(2) Transport and inventory costs
A couple of thousand of these stand up bags can fit inside a large carton. A couple of thousand plastic bottles, depending on what size they are, will at least need a small room. This increases the costs of storage. A consequence of occupying more space is that a business has to pay more to transport plastic bottles from location X to location Y. So stand up bags are a winner here.
(3) Environmental friendliness
It takes more resources to produce a bottle of plastic. A plastic bottle is not recyclable. It occupies more space in a landfill than a plastic pouch, therefore requiring more landfills. It takes a lesser amount of plastic to manufacture a stand up pouch. These pouches are recyclable and are landfill friendly, which means more of these pouches can fit inside a landfill – thus requiring fewer landfills. So stand up pouches are a winner here too.
(4) Usability
On the face of it, a plastic bottle appears to be more user-friendly. It fits inside a knapsack, it is strong, and it doesn't break on falling. On closer look, it is apparent that with accessories like a spout, a stand up pouch becomes as usable as a plastic bottle. It fits inside a bag, and you don't need to have an extra pocket for it. Unlike a plastic bottle, it doesn't puncture or burst on falling. Usability is more of a subjective issue. There are people who find typewriters more usable than modern computers. So let's call it a draw here.
In these four comparisons, three are won by standup pouches, and one was a draw. So we can safely assume that plastic pouches are better than bottles.