I think it’s a terrible way to decide the winner. For example if player A won the first set 4-0 then lost the second set 3-4 they would have won 7 games to their opponents 4.
I've always thought this was kind of a dumb argument, albeit an intuitive one. As BRussell already pointed out, this is always a possibility with sets, so if you have a big problem with this, then you have a big problem with multiple sets ever being played anywhere by anyone because this will always--always--be a possibility with multiple sets. Something tells me you aren't actually opposed to multiple sets being played by yourself or others though and that it was just a knee jerk reaction excuse you latched onto to try to justify not liking it for some other reason.
The "but you could win more total games and lose a best of X sets match" argument is in my book akin to the 4th place finisher in a tournament being salty about and complaining about how they won more total games and/or a higher percentage of their games than the winner of the tournament did, and now they are somehow feeling that the format cheated them and they should be the rightful winner of the event. It's silly thinking. Here's the bottom line. They weren't playing for the most total game wins, or the highest percentage of game wins. They were playing who would win all the sets that would ultimately take them to a first place finish, just like in your example they were essentially playing for the best two out of three sets (the third set is obviously a different type but still essentially a set), not the most individual game wins in all the sets.
It is also somewhat akin to a player in a race to 100 complaining that they were literally never behind during the entire set and yet they lost the set because their opponent tied it at the hill and then won the case game. "I was ahead for literally 99% of the match, and yet my opponent is being called the winner, that's BS, I'm clearly the better player as I was leading the entire time". Thing is though you weren't playing for who could spend the most time in the lead, you were playing for who would hit 100 first, and it wasn't you.
You have to win the game that you are playing, not some other game or stat you have made up in your mind which makes no difference whatsoever. Trying to come up with some other format or stat you would have won under is mostly just coming up with excuses to try to make yourself feel better for not having been able to come with it when it was needed so that you could have actually won under the format that you were actually playing.
Pool should be decided by playing whatever the game is.
That is a whole separate topic entirely that you are somehow trying to link together. There are reasonable arguments to be made for staying with the same game always, and also for altering things in an attempt to create sudden death type pressure and excitement. It's personal preference, but what I can say without doubt is that a lot of what pool players like is because that is what they are used to, and if they also got used to something else they might like it just as well or even better. There is almost no doubt that many people will come around to liking this format change once they get fully used to it (and you already see it happening), the only question is will it be enough of them to justify using this format long term? Time will tell, but keeping in mind that more people are going to come around as they get used to it (and seeing the verification of this actually happening) we should probably be willing to give it some time and see how it ultimately ends up shaking out.