Class spell lists belong with their classes.
I agree on this. Much better to have "Clerics spell list by level" in the Cleric chapter rather than clump all class spell lists in the Spells chapter.
Specialties were much better with their feats underneath. (Of course that requires that all feats only belong to one speciality.)
Well this is an example that proves it isn't an easy choice... Those groups who use feats but not specialties would have to remember where to find each feat. However this is PC's material so each player only has a few things to remember, and they are going to be written on the character sheet.
Even if all Yuan-ti do constrict, "Yuan-ti traits" is not enough.
If the game is going to be stable for at least several years before getting a revision, then they can drop the "monsters type traits", because those are mostly useful in a game is revised continuously, so that they can update the traits of all creatures in one go.
Otherwise I think it's actually better to have no common "traits" that work as absolute bounds i.e. apply to really all creatures of the same type. For example, do we really need all undead to have darkvision? To be immune to criticals? Maybe a very few traits can be common, but then if they are really few, reprinting them is not a big deal.
I would still like to see a MM divided into chapters by creature type, but then the common text can be more about the
common story* rather than the common mechanics - and for instance,
certainly the idea that all creatures of the same type must share hit dice, skill points, saving throws and attack bonuses is going away!
* such as "what is an undead? what kinds of undead exist?", "what does it mean for an elemental to be alive?" or "where do feys come from, why such different creatures are all called fey?"