I had an idea about addressing the Wondrous Effect, it's a bit rough, but there's a couple of points to it. Currently I think there's a couple of large issues, Wondrous Effect stands as too strong on its own and Patronage is almost purely Scientist affair, as both influence and industry cost of Manufactories is negligible. It's also a 0-1 type of affair, you research the tech, you plop down Manufactories you are eligible to and then, only if the map is big enough, there's two, maybe three luxuries left in the world on some remote islands that you can claim at a later date.

Make Manufactories cost a lot more Industry and a Shared Project

First, you should be able to build Manufactory for a single copy of every Luxury Resource within your city limits (no longer buying them out with Influence, but we'll be back to it in a moment), but make them costly projects that would require dedicating a couple of turns in multiple city queues.

Give every Manufactory an 'Improved Effect', that is a lesser version of Wondrous one

Now hear me out, when you're done with building it up, it no longer grants you a Wondrous Effect over that resource (that's why you are able to plop them down willy-nilly). Instead it gives you now a 2-3% of related FIMSI per source (a portion of Wondrous Effect) and no Stability aside of Manufactory itself providing some on its own as a building (+10? +20?). Wondrous Effect on its own should also provide diminishing returns of Stability, IMO, +10 for first copy, +5 for second, +3 for third and only +1 for every consecutive one.

Introduce a new tab for Wondrous Effects, where we could use Influence to buy them out

Here's how I want to address one of the biggest gripes. Once you've built your first Manufactory a new tab should open up for you (maybe accessible when clicking on the Luxuries list, maybe another button next to Wonders), with all the Luxury Resources you have Manufactories of highlighted and current amount required for Wondrous Effect. It's 1 by default, but once someone with, for example, 2 copies of that resource within their borders claims it (utilizing Influence), this number goes up to 3. So it would turn into semi-active race, while being blocked out of Wondrous Effect wouldn't be the end of the world either. Once again, only sources in your territories would count, copies bought would only serve for improving the Effect, not claiming it.

Thoughts? I can see this being a bit too much to juggle on faster game speeds, I do admit most of my ideas come from playing the game on Endless. There's also an issue of Money, paradoxically, being left as one FIMSI (aside of Food, but that one technically would be in as a way to rush the Manufactory?) not used in this mercantile game concept, but then again, you use it to acquire more copies of Luxuries once Improved/Wondrous Effects are in place. I also think that amount of copies required in the new tab should be dynamic, so that it goes down once owner losses a copy, but also goes up if they acquire a new one.

There's also an issue with Trade Resources in Material Procurement Civic, but maybe it could offer an Influence discount on claiming the Wondrous Effect or add a point of Stability for every copy of Luxury you have at least an Improved Effect on? Or flat out Money discount for buying Resources with at least Improved Effect?

Increasing the industry cost would push the game a bit more, once again, towards production. At least, in the present iteration, science is here the main driver.
The rework of the Wondrous thing seems an improvment.
I like the claim with influence, as it makes it a bit more useful but am not sure about the race thing.

I guess, what I like the least about the system is its exclusivety.
I'd rather rely on having access to some resources (at least X%) on your territory to get a manufactory going, but without restricting it to a single player. The bonus could be adjusted by the amount of resources disponible and be bought with influence but without any fear induced by a race.
If you wish to keep the racing part, »buying wondours effect« could increase worldwide for each resource, never being taken away from a player but still rewarding the fastest.

Phew, I missed this thread when you posted it, DLNH.  Thanks for sharing it in the "Remove Luxury Manufactory" thread.

DNLH wrote:
Make Manufactories cost a lot more Industry and a Shared Project

I like this idea, not only because it would slow down an empire from rapidly buying out all available Manufactories the moment they learn Patronage, but — whether you intended it or not — it could add the limitation that your whole empire can only work on a single manufactory at a time.  I'm thinking of times when I haven't been building all of the Holy Sites I'm allowed by having a high Tier Faith, and even if I have 2-3 Holy Sites to build, I can only create one at a time.  Collecting all possible manufactories into a "Manufactory" shared project that takes a few turns to build would keep the first empire who reaches Patronage from spamming out all their manufactories in one or two turns.  However, @Cure_off makes an excellent point that this again benefits industry.  Admittedly, a lot of the game necessitates industry, and the way patronage currently works could be considered a counter to that and a benefit to science.

DNLH wrote:

Give every Manufactory an 'Improved Effect', that is a lesser version of Wondrous one

Now hear me out, when you're done with building it up, it no longer grants you a Wondrous Effect over that resource (that's why you are able to plop them down willy-nilly). Instead it gives you now a 2-3% of related FIMSI per source (a portion of Wondrous Effect) and no Stability aside of Manufactory itself providing some on its own as a building (+10? +20?). Wondrous Effect on its own should also provide diminishing returns of Stability, IMO, +10 for first copy, +5 for second, +3 for third and only +1 for every consecutive one

I like this idea and have a slight alternative that would do away with the larger "Wondrous Effect" entirely and would break it down into an "Improved Effect" like you've proposed:  

What if the Manufactories unlocked by Patronage were "lesser manufactories (compared to their current form) that unlocked +5% F/I/M/S for the luxury tile exploited by that manufactory?  Do you have two deposits of Dye in your territory?  You can build two lesser Dye Manufactories on them, and each of them nets you +5% Industry and +10 Stability* on all cities per manufactory for a total of +10%Industry and +20 Stability*.  That also means that another empire with three dye deposits can build their own three dye manufactories for +15% Industry and +30 Stability.  There would be no global monopoly on a wondrous effect except for maybe the Hanging Garden.

Essentially, this would make a manufactory a "Tier 2 Artisans Quarter" and whose "Improved Effect" cannot be shared through trade.  Empires would just naturally begin to get a boost from the luxury resources they control in their Early Modern Era, and they can still trade luxuries for basic benefits.  The other consequence of this is that nobody gets a lock on the Wondrous Effects of a dozen resources by rushing Patronage.  Empires could also continue to fight wars and jockey for control of these "lesser" manufactories, as collecting more would still be worthwhile to control throughout the game.

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(* I think +10 Stability per Wondrous Effect is too high, but I've kept it the same in my example here because my proposed change is about breaking the bonus down and getting it in smaller pieces.)

I like the idea of improving every resource individually, but this would be essentially doing away with Wondrous Effect altogether. Maybe it is the way, rather than trying to salvage it, cut it off completely. I feel a bit icky about it, as it is one of the few largely peaceful interactions that are in the game, but as they will be a focus of next expansion, then maybe it wouldn't be that big of a loss. And as it is now it's not much of an interaction either.

I still think that main issues with Wondrous Effect are that it is 0-1 and set-and-forget type of thing, once you get access to it you turn it on almost instantly and once you turned it on nothing aside of war or a raiding party (gods know I had IPs do this to me once or twice, boy, was I fuming when I discovered that manufactories can't be rebuilt) can take it away from you. I'd very much like to keep the ability to contest the Wondrous Effect and I still think it makes sense, but I see how this may not sit well with all players. You'd still be able to secure it relatively safely by having majority of sources and the Improved Effect was supposed to mitigate the missing out on Wondrous one. If anything, I'd imagine it would be less of a race, as you could actively take the effect away from someone who claimed it first.