I always build Aqueducts when I see Plague breaking out somewhere.
You know, we really could use the +1 specialist per specific improvement mechanic for buildings a more often. It's a simply XML thing so no coding required, and I know FFH's Magistermodmod spams it for almost anything.
We need to address the balance of civics btw. I noticed that the main reason for the watermill's current weakness lies in the relative overpoweredness of Farms and Workshops with the Agrarianism and Guilds civics. While I can understand the former since we need something to be competitive with Slavery before the Renaissance the latter is overpowered. There is simply no reason not to adopt Guilds as early as possible and stay in it until Free Market or sometimes even Central Planning comes along. The problem is that its only alternative before then is Mercantilism, which while greatly improved from its Vanilla implementation is still inferior. In fact I think I even saw a thread about its uselessness recently.
The removal of the Watermill's second commerce didn't help matters either, but since that only applied in the late game we can ignore that for now as I want to talk about the Medieval to Renaissance improvements balance first.
Currently, if you have two tiles to improve and want them to be food neutral you have two options:
Farm + Workshop: 3H1C
2 Watermills: 2H
As you can see the former combination not only gives a higher production output, it throws in some commerce as well. That it also takes fewer worker turns to build is just icing on the cake. In this scenario one could argue that workshops plus farms are easily twice as good as watermills.
(I'm ignoring Cottages on purpose because they are a special case, and while one can easily argue that they are underpowered as well they are not my priority right now.)
Let's compare this with how it would look in Vanilla, or let's just say before the current implementation of Agrarianism and Guilds:
Farm + Workshop: 2-3H
2 Watermills: 2H
Even back then Watermills were slightly worse actually, but at least there was nothing boosting farms and the civic giving an extra hammer had real competition, so if anything Leoreth's nerf of the Watermill just reinforced an already existing unbalance. And if we want to get technical and ignore the halving of its commerce output, he didn't even make the Watermill itself worse, he just made every alternative better.
Now there's two ways on how to solve this: Either we redo Agrarianism and Guilds completely or we slightly boost Watermills, say by giving them +1 Commerce with Engineering. Assuming we go with the latter and return to our thought experiment of having to improve two tiles while staying food neutral, 2 Watermills now give the exact same yield as a farm and a workshop combined if we assume that one hammer equals one commerce. Actually, in most situations that is not true and one commerce is actually worse than one hammer, but at least now one could at least think of a scenario were two Watermills outperform a workshop and a farm, and that is you have too many workers lying around and value commerce over production, but not so much that you'd rather build a cottage.
Conclusion: Watermills are currently so weak that even if we gave them +1 Commerce with Engineering, which would have been my favored solution apart from making them ridiculously overpowered provide realistic yields as in my self-deprecating totally historical mod, they would still be worse than most alternatives.
My proposal: Do something about the Guilds civic. Either remove the +1 Hammer for workshops or make another civic in its timeframe competitive. Heck maybe we could try removing the +1 Hammer from the Guilds technology instead. You know what, let's think that through while assuming Engineering provides +2 Commerce for Watermills:
Farm + Workshop: 2H1C
2 Watermills: 2H2C
There, now the latter for once provides a higher yield than the former. Since Watermills require more worker turns to build than all other non resource specific improvements apart from the fort, this is the first scenario I proposed in this post which is actually balanced.
While I'm in the mood, let me just put up the following suggestions as well:
Cottages now consume workers upon being built. This gives a nice new hammer sink to help with the lategame overproduction issue. To make up for it Towns now give extra defense and act as cities for resource connection, naval and aerial unit movement and combat purposes just like forts, and provide +1 Hammer with some lategame tech.
Lumbermills get moved to some late Classical or early Medieval tech, so the player actually has some tangible benefit from not chopping down every single forest in sight immediately.
Returning to my thought experiment from before the situation would now look like this:
Farm + Workshop: 2H1C
2 Watermills: 2H2C
2 Lumbermills: 4H
Hmmmmmm actually now Lumbermills look overpowered, but on the other hand you don't get the 30 hammers chop boost if you build them, so now it should be an actual choice between short and long term gains.
Forest Preserves should provide +1 Commerce and gain another with Mass Media or Ecology. Currently there simply is no reason to build any of them whatsoever outside of your National Park city unless you are running Environmentalism. Also they should spread irrigation.