D&D 5E - Princes of the Apocalypse: New DM bouts about progression and late dungeons

But it’s mostly because the book’s organization is awful.

There is only one explanation that makes sense: I have read that PotA was originally planned as two separate books, one being the main adventure and the other a setting guide with player options and the various side quests and level 1-3 material. When the decision was made to combine these two products into a single book,* very little reorganization was performed.

[*Actually, it remained two books in a sense, because the Elemental Evil Player's Companion, available as a PDF or DM's Guild Print-on-Demand, presents all the new player options as well as the new spells (which were also printed in PotA and were then reprinted in Xanathar's Guide to Everything). But the majority of content of the two originally planned products was (poorly) combined into the one main book.]

A DM using the print version really needs to spend an hour or two pencilling in page number cross-references throughout the volume, because information on all kinds of things is split between two or three sections, often with no indication in any of those sections that the reader should consult the others. If WotC had put a little effort into reorganizing the module after the decision was made to combine the two books, the final product would be much improved.

The other big problem is this:

As others have mentioned, there’s a tension between the sandbox nature of the campaign and the fact that each area is designed for a specific party level. Now, many have argued that sandboxiness and encounter balance are simply noncompatible virtues in general, and there's something to that argument—but with PotA, the design of the module brings these virtues into even greater conflict than is usually the case.

Here's what I mean. The four Haunted Keeps are each balanced for a level from 3 through 6 and are meant to be encountered in any order. Similarly, the second "tier" of locations is keyed for levels 7 through 10, but also can be confronted in any order; and the same is true for each of the nodes with levels 12 through 15.

I agree in principle with the notion that encounter balance shouldn't always be the same—it's OK to have players confront both easy-peasy and very difficult challenges over the course of a campaign. But the way PotA is structured, we're talking about whole, large areas, not just one-off encounters. It's one thing to throw a CR 7 encounter at a level 10 party; it's a very different thing to expect a level 10 party to enjoy plowing through session after session of too-easy encounters clearing out a large level 7 dungeon.

The ideal solution to this problem is obvious: each of the Haunted Keeps should be provided with suggested adjustments for each party level from 3 through 5, and so on for the temples and for the nodes. This way everything within a tier really could be confronted in any order and yet still pose an appropriate challenge. You're still stuck with the problem of whether or not to let the party into a new tier of dungeon prior to confronting all four locations in the previous tier—I lean toward "locking" the access points as Sly Flourish recommends.

(Of course, Sly Flourish states in the same breath that "the world shouldn't shift itself around to suit the level of the PCs, and again, in principle I agree, but in this case it makes perfect thematic sense since each cult is supposed to be trying to build its power over time, recruiting new followers, etc., and because the cults are in competition with each other, so while the PCs are damaging one cult, the others would be able to strengthen themselves.)

Adjusting the area level is especially important when it comes to the temples and nodes, because the PCs are likely to stay in each of these areas until it's clear, and that means session after session of potentially quite difficult encounters followed by moving on to an area consisting of many sessions of quite easy encounters (or vice versa). I think it's much better to have either consistently baby-bear porridge, or else a nicely varied mix of temperatures. And of course, if you run the finale of the adventure as written, then the question of which Prince you confront is determined by which node you confront last, and yet, again, the nodes are balanced in a particular order of difficulty.

As with the organization problem, it's totally possible for a DM to make these changes. But it would have been even better if they didn't have to do that work.

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