The problem with that is that newly founded cities with only one pop had ridiculously high excess health and happiness in the old system. Don't you think building infrastructure should be rewarded?
That's exactly the point. Health from grain resources was just too readily available as it was. Many civs have two of them within reach and with the obligatory Granary that was a lot of free health.
The thing is that in RFC, health resources are placed very liberally to allow high population when cities are close together. This not only means that civs tend to have a lot of them in their native area, but also that if you lack it, they're easy to trade for from those who do.
In consequence, health was really only something you had to manage during plague or as a jungle civ. Which is not really what vanilla BtS is like. With rainforest becoming a thing in the foreseeable future, the latter will not be as much of a factor. And I'm willing to reduce the plague unhealth if required.
So these resources exist mainly to provide food, not health, therefore it makes sense to cut their health effect in half.
On that note, maybe we really should remove health from grain resources from the Granary, as it is already the most important building there is, and move it to the Market?
Now how the health effect should be cut in half is still up for discussion.
The current decision was mostly motivated by seafood, because it makes sense to only have coastal cities benefit from seafood. The effect was moved from lighthouse to harbor to not delay it too much.
In general, I think it's more important to encourage infrastructure than handing out health for free. Actually, I hope this will make Aqueducts actually relevant in the game.
I don't really get why is it brought up that Granaries are either free or built anyway as an argument against this. If anything it makes the argument kind of pointless.
Now for the relative health of livestock versus grain. I don't really care that much, but if I cared this is the argument I would make. Grain makes up most of the world caloric intake exactly because it's a staple food. Grain keeps you fed, but it doesn't make you healthy. That's what everything besides staple food is for, meat, dairy and the like. I could add a link about skeleton comparison for hunter-gatherer compared to agrarian societies here but as I said, I don't care that much.
For most of the game, there even isn't an effective difference, as Supermarkets come so late. If anything, the previous situation where grain was more valuable for most of the game was more unrealistic. And afterwards? Just goes perfectly with the "late game population boom" argument, doesn't it? Not that this is in any way related to the topic.
Is Granary too powerful now? Well it hasn't actually changed in absolute terms, but in a relative sense maybe. I don't want to move health from grain further down the tech tree because that would become harsh (Market and Currency is very late imo). Not against splitting the effect into two buildings though.
Aztecs now are in even worse position, making their 1st UHV almost undoable! Given that England and Japan know compass by 1520, that's what happenned:
England lost 1 health bonus (wheet).
Japan lost 1 (rice).
Aztecs lost 2 health bonuses (crab, fish).
I don't see where you get these results, all of them lose one grain and two seafood health. England has fish and crab, Japan has fish and clams.
Still, I'm aware that the Aztec UHV is tough and luck dependent with European and Asian competition. I plan to address that, which is exactly why I got this change over with before that.