"But my question is, would fans be pleased if Nintendo implemented a security system that was very safe but EXTREMELY easy to use, like instead of 16+ number friend codes, use 4 or an user created password?"
Hell I would be fine with one 16+ number for the console, like a phone number. The fact that it's a game-by-game basis is the most annoying part. Just because Nintendo's service is free doesn't mean it has to suck. For years PC games have offered free online play. It doesn't have all the bells and whistles of Xbox Live but that isn't needed to have a good online setup, just having a logical match-making service.
Nintendo's implementation has nothing to do with cost. All this friend code nonsence isn't to save money. I don't even think it can save money. It's just a way to do things and unfortunately it's a really awkward inflexible one. Having a fee would just result in an awkward inflexible solution that costs money.