I have pondered similar things leeday100196 but the situation (which in your defence was not really covered earlier in the thread which was more a discussion on advertising) as I understand it
First it should be noted paypal have resisted becoming a proper bank/money handling service everywhere they could (which at this point includes the US which is the base of their operations anyway I believe* and the base of operations for subsidiaries of other big companies relevant here) and done the bare minimum elsewhere which is not something that encourages hope in me. This said along the way they somewhow became both trusted and almost the de facto online payment method (and to be fair what I have seen of their API, agreements and such vs the stuff banks, Visa and co had at the time I can see why they were opted for) to the point where some would consider not supporting paypal a mark against a service/shop. From what we have seen it seems Nintendo has wandered up to paypal and said "these stores... best if you do not offer your services to them" which at best is legally dubious (there have been some cases where flash cart vendors have been taken to task up in front of the beak but nothing that resulted in an unequivocal ruling) and at worst is a straight breach of ethics but as just covered as paypal are not a proper financial services company and in this case are technically free to do what they like (this said even proper financial services companies have serious leeway as seen in the whole visa/mastercard wikileaks thing). Being a de facto monopoly, to say nothing of paypal freezing accounts which includes liquid assets of a company (your company can be worth a lot but if you take what seems a fraction of that money out of play it can leave you in the lurch), a lack of paypal tends to make for a lack of sales for whatever reason.
*I am way too lazy to bother figuring out the corporate structure of paypal or indeed ebay and reconcile that with financial services laws.
