Like any Company, Sony is concerned about its bottom line. Especially after the last few years when they've been in the red. However, Japanese companies in general, Believe that a healthy bottom line is the result of good customer relations. Buying a cell phone in Japan is a two hour endeavor, every Little detail will be explained to you so that you can utilize it to the fullest when you leave the store. Bloatware for example are rarely apps, just download shortcuts, so if you don't need or use a certain app it never takes up more than 20 kB on your phone. Japanese vendors consider this part of customer relations.
I have no details of the Sony - Kobo deal, but from my experience working in a Japanese company, I feel fairly certain that Sony's primary concern in cutting the deal was to not leave customers hanging. Either they have provided Kobo with access to the firmware or promised to implement any changes required (probably for some sort of payment) over a certain time span.
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