Wine has to duplicate all of the duct tape and bailing wire Microsoft has used to provide backwards compatibility for their customers' existing applications. Just as Wine is an important kludge serving as a compatibility layer [It's Not an Emulator], all those undocumented API's are the same sort of kludge as compatibility layer.
And of course Wine is an outlier. Not only in that it contains its own 20 years of legacy code but in the fact that it is black box reverse engineering. It can't use disassembly to suss out details. Wine's difficulties stem from its requirements as much as anything else. These days VM's are the way to go if the going is intended to get things done. A Windows box in the cloud is pennies per hour.
So far as I am aware, ALL usable operating systems are burdened with that sort of thing. I'd really like to see someone at least attempt a clean-slate OS. Make it 64-bit only from the start, vector fonts to support HighDPI displays from the beginning, etc. It would likely accumulate such cruft over time, but I would expect there to be substantial advantages to building from scratch something that rolls in all of the research advances and assumes capable modern hardware.
And of course Wine is an outlier. Not only in that it contains its own 20 years of legacy code but in the fact that it is black box reverse engineering. It can't use disassembly to suss out details. Wine's difficulties stem from its requirements as much as anything else. These days VM's are the way to go if the going is intended to get things done. A Windows box in the cloud is pennies per hour.