Personally I think its a good idea to have such a limitation, as you need to make more strategic choices with buildings and cannot just build every building everywhere. While value for money is a thing, there are also a lot of flat modifiers - having a +2 / +4 force limit building in every province kind of makes that all non-sensical. I think the choice should go beyond "is the building worth the 100 gold"?
The new manufactories buildings where the choice is even harder are a very interesting addition.
Question is if the values are still correct - especially in terrain that is less favourable towards buildings. There are now more buildings available in general and most importantly courthouses are now far more important. Increasing the base value by one would reduce the problem.
I'd appreciate an option to delete buildings by type in the macro-builder as well.
As others have said, most of the buildings aren't worth building in most provinces anyway unless they already have 10 Dev and 0 Autonomy so removing building limit wouldn't change much, if anything. Ducats and ROI are already the main constraints when choosing what to build and where.
Now, regarding the ship/FL buildings, why are they an issue exactly? In SP you are never hurting for FL if you have enough ducats to increase your FL by buildings barracks (I think that's the name of the FL building). It could be different in MP but I have next to none experience with that game mode so I won't say anything regarding it.
Now for naval FL. It is an absolute joke -- simple as that. If you need more ships than your FL can support than you will either just build them anyway because the ducat cost for going over naval FL is so very small or you won't have enough sailors to support a larger navy. I find that sailors are always my naval soft cap and that I never have to worry about naval FL. You either have enough sailors or you don't.
So, how would removing the building slots really affect the game?
Why should a shipyard prevent me from building another shipyard?
Buildings are a joke. Their value and usefulness assessment is either trivial (temples) or a pain in the ass (manufacturies).
Unless, you're not min-maxing. Then they're just pretty pictures.
The building system is an absolute joke. I'm the type of guy who loves RTS' and city building games but I don't mind having an abstract building system if it better suits the game (like in EU4's case). That said, EU4's take on buildings isn't really an abstraction nor "immersive". It just is.
You can only build one of each building per province, meaning that you are either building A Building in a city (which brings up the issue that you deal with provinces and not cities) or you are building one heck of A Building in the province capital. I think that the first option is much more plausible when you take into account how City used to be part of EU's terminology and the line between city and province was much more blurred back in EU3.
Gameplay wise, buildings serve two functions: A) increase resources as time goes by (ducats, manpower, naval power, trade power); B) make stuff cheaper (Dev cost and GC). The existence of building slots constrain the system too much as it is always more efficient to build manufactury -> courthouse -> workshop -> temple/fort -> everything else. You already get a poor ROI and things like trade power and manpower can be acquired easier and cheaper by other means than buildings so why even bother with those options most of the times?
And then you get the issue of having to delete buildings per province and not having an easy way of knowing what is built where and having to navigate through menus to find stuff. Granted the macro builder is good but it leaves much to be desired.
All in all most buildings only exist to exponentially increase your ducat income and the rest as situational at best.
I still miss EU3's unique builds which you could only have one of each and they would give you some cool stuff like more diplomats, prestige, army and naval tradition, etc.