I think lack of uniformity in 5e is in general a problem.
Subclasses in different levels with different classes means you cant have an universal subclass shared between several classes.
And even with classes sharing the levels they gain subclass features (like monk and ranger), the power budget between class and subclass is soo widely different that you cant do it as well.
I strongly agree with this and the next few posts.
Universal subclasses are in theory possible but retroffiting that on top of 5.Xe would require so much work that the end result might be unrecognizable, and all the tradeoffs made along the way may be a bitter pill to swallow. It would basically be 6e (and D&D doesn’t have it easy with even numbered editions…).
Rather than building 6e, I think there is a 5.75e within reach, and it takes us full circle back to the OP… "prestige feat paths" can be tacked on in a compatible way, that doesn’t require redesigning everything, and is fully optional. Those who don’t care for it can safely ignore it.
Subclasses are well-designed for extending the classes and hooking into class-specific mechanics. The EK can have Arcane Charge because the Fighter has Action Surge. It makes no sense as a generic or univeral thing, but it fits perfectly as a subclass feature.
The alternative, "prestige feat paths", can be for things that are intended to be more universal. The Mage Slayer feat is useful for many different builds, and that’s why it’s great to have it as a feat and not as a subclass feature. It could become the entry point of a "Mage Slayer Path" by being the prereq for a handful of other feats. Those other feats should either be based off of a class-free mechanic (e.g., Proficiency Bonus) or else have some sort of scaling factor that relates to the feats themselves (e.g., "you can use this ability N+1 times per short rest, where N is the number of feats you have with Mage Slayer as a prereq" or something like that).
Feats are the flexible mechanic that is most decoupled from classes, and that is why I view them as a logical choice for building on top off.
Doesn’t mean there needs to be 300 new feats. But the subclasses that don’t really fit as subclasses, because they are not hooked into their parent class’ features, or because they are relevant to many classes, could be converted into feats and available via either mechanism. But more interestingly, rather than bloating the subclass catalog, future subclasses should be considered for designing as prestige feat paths instead.