This is a problem with most large companies. Once you reach a certain size, you encounter problems with scaling. Paypal is such a big company the only way they and other companies like them innovate is by acquiring other companies and teams because it's cheaper and easier.

The amount of friction within a company like Paypal I would imagine is quite high. Not even those at the top of companies like these can change things at the flick of a switch. Things move very slowly in large companies, this is why smaller startups are able to come along and shake things up so easily before being acquired. It is how it is.