My advice - stop treating production like something you get for free. There are huge bonuses to be picked up, and they'll benefit you more the earlier you build them.
It's not free, it's an investment.
If you notice, I was specific in my example with the +1 PPM bonus of Timber Mill. Logging Camp is fine. In fact, my mod uses Logging Camp as a mold to make the other production options equally as desirable. Lumber Yard gives me 1200 or so extra production by turn 500. There are very few things I can buy for 1200 Production, maybe one extra unit. Is that all we want out of an upgrade? One unit? A semi-costly building? Some very small rocks? I say no. I say we should be getting a return with in 50 seasons of construction. +1 PPM is fine if the cost stays at 80 production. At +2 PPM we will start to see a much better investment potential and more labor makes sense. Timber Mill is just atrocious. It won't ever pay off in time to offset the cost on not building better choices earlier.
It really comes down to Production needing to compete better with the other choices in the system. Considering how much you can get from going straight to the things you want, instead of investing in getting future things faster, many later tier production options just don't add up. I can see how you might think so though, if you were under the impression that each one added an extra 3 or 4 production on top of the previous improvement. That would be a good deal.
I think 3 Materials should be the mean on which the balance is decided. Having more should mean better payoffs, while having less would mean you might never see any profits. It's a good balance and adds some significant choices. Choices that can be debated for years to come.