I'm perfectly fine having both sets of rules. I think it makes for a better fan experience.
When it comes to watching non-Red Sox games, I actually prefer watching the National League. This isn't because of double switches or sac bunts, but because the game has a natural ebb and flow that makes for a more tense viewing experience. When you watch an NL game, you really have to track where each team is in the lineup. You begin to notice that certain earlier innings can take on massive importance, such that they end up feeling like the 8th or 9th innings. Say the Cardinals are losing to the Cubs 2-0 in the fifth inning, with their 3, 4, and 5 hitters due up. That fifth inning becomes massively important, because you know that with the pitcher's spot coming up soon, they're not going to have as good of a chance to score in the 6th. If they can't tie the game or take the lead in the 5th, they're going to have to take out a starter who's actually been pitching pretty well, and they're not really going to have another decent chance to score again until the 7th or 8th.
You don't really get that rhythm in an AL game. Sure, any inning that starts with your 3, 4, and 5 hitters is going to feel like a great opportunity to score, but the sense of urgency isn't quite there because you don't have an automatic out coming up in the 9 spot, and what you do offensively that inning isn't going to have as much of an impact on what you'll need to do with your pitching. In an AL game, it feels like 6 runs can go on the board at any given time. Whereas NL games have the rhythm of a roller coaster, AL games just move along like a steady train.
Having said that, there are also things I prefer about the AL game. I think it sucks, for instance, when an NL starting pitcher gets taken out of a 1-1 game in the 7th in favor of a pinch-hitter.
I'm glad I have both options as a fan.
As for the World Series, I just don't see why anyone gets so worked up about it. It's a minor difference that both teams have to adjust to in the same way, and that both teams did already adjust to during the regular season. There's zero evidence that it does anything to make the Series unfair or illegitimate in any way, and, again, it provides for something more interesting to keep an eye on as a viewing fan.