So the question because, first, what exactly is it about the disjointed system that you like? And from a designer's perspective, how far do you go to achieve that, before you start opening up the sort of problems implied by the two fully disjointed systems? Because if the answer is just something like, "I like the ability of the DM to freeform a monster without having to worry about if it is 'right'.", or "I like that monsters are conceptually simpler than PCs", I personally don't feel that it's essential to not have some sort of systematic approach in order to achieve those two results and ultimately make everyone happy.
3e is the only version of D&D where PCs, Monsters, and NPCs all shared the same structure. Therefore, I'll address the failings of such a system in terms of 3e (and its children).
I don't think its fair to dismiss simplicity of play or complexity of design as unworthy goals. Both are very important to a LOT of DMs. As a Pathfinder DM who has reached mid-high levels (9+), I can tell you the complexity of making NPCs and monsters using the PC Gen rules is tedious. To whit: the last three "major" opponents my team has faced has been a Red Dragon, an NPC rival party, and a Lich Cleric. The creation of each encounter by scratch would have taken dozens of hours. Each required building a creature from the ground up: skills, feats, HD, saving throw DCs, and the holy mess that is NPC equipment. The only reprieve *I* got was that PFd20SRD.com has dozens of such monsters pre-done for me; I only needed to swap a race here, a domain there, etc. Building these encounters from scratch would have required probably a full day of work per encounter.
Likewise, there is a lot of chaff abilities that clutter up said statblocks (which is to say, class abilities that look fine on a PC's sheet, but do an NPC no use in a one-encounter lifespan). For example: the NPC sorcerer (for story purposes) had the shadow bloodline, which granted him a bonus to stealth checks when he cast a shadow/darkness spell. Neat ability for a PC, mildly useless when the sorcerer's primary function is to shoot illusionary fireballs at the PCs. Likewise, I was pretty pointless to give the Lich the magic-domain abilities since he was mostly just using undead-boosting spells anway, but a cleric's gotta have two domains. All of these options get in the way of making the encounter smooth.
Likewise, you don't need complex monsters to clutter up the system. Feats do that job from level 3 on. Most giants have awesome blow as feat; can you tell me (without looking it up) what it does? Its bad enough to have to do that with spells, but feats just added headache. (It gets even worse when you go further away from the core: there is a monster in Libris Mortis whose primary abilities are hidden in its feats which were new feats in Libris Mortis's feat section. I think it gave penalties every time it hit or something. Anyway, if you didn't know what "draining strike" did or indeed that the monster even had it; it was severely weakened). Pathfinder wins the award for least convenient though: they put abilities in Feats, Spells, and Universal Monster Abilities. For some monsters, I've needed to keep the PRD open on four tabs (stat block, feats, spells index, and UMAs) just to run one monster! Heaven help you if he has a magic item...
Speaking of which, can I say NPC math sucks? Monsters can be built around front-loading HD (which raises saves and bab, as well as hp) and you can cheat natural armor scores to get proper ACs, but making a human fighter a challenge requires him to carry an array of magical do-hickeys (magic armor, magic weapons, cloaks, rings, amulets) just to bring his numbers up to CR. And what does the group DO with said do-hickey which they already have one of or better? That's a different discussion. Suffice to say, every pawn shop in Waterdeep has an amulet of natural armor +1 to sell ya...
Of course, the natural answer is "But Remy, you don't HAVE to account for those amulets of natural armor! Give him the AC that fits and fudge the numbers! Forget about silly flavor abilities like shadow bloodline arcana, focus on the important stuff. Don't give monsters complex feats (I hear Improved Initiative, Toughness, and Weapon Focus are nice) and don't worry if their skill points equal 6+ Int Mod." But that's what 5e does. So the solution to the problem has been found. Ignore the crap, build NPCs like monsters, and only focus on the important things.
Tl;dr version: 3e's insistence in making PC, NPC, and Monster math work the same created a lot of problems creating and running complex encounters. Attempts to simplify the process inevitably lead you back to diverging the math. While I do think some additional guidance on making monsters and NPCs in 5e would be nice, I can't imagine going back to monsters being PC-level complex to build and run again.