When 4e was coming out and Paizo had to decide what they wanted to do, part of the justification for sticking with the d20 edition of rules was because they didn't feel the 4e rules, as they knew them thus far, enabled them to build the stories/adventures they wanted to build.
This is an interesting commentary, and I remember hearing the same thing. I've done quite a bit of converting from earlier editions to 4e. What I have found is that the adventures "play" much better in the 4e ruleset, than in the original. Keep in mind that my conversions very rarely change the "behind the scenes story." So it it interesting that Paizo "couldn't" tell/build the stories/adventures they wanted when I, and others, are obviously using those stories with little change.
IMO, Paizo recognized the same thing that Green Ronin recognized when WotC changed from 3e to 3.5. If you hitch your wagon to the WotC horse you are inevitably tied to go where WotC decides to go, and WotC will do what is good for WotC - regardless of how many wagons are tied to their horse. Green Ronin created their own games and Paizo decided to do the same. A small publisher has a greater margin for success/failure and is much more flexible than a behemoth like WotC.
I did want to hear, as a converting 4e DM, your perspective on these questions and how 4e make you think about encounter/adventure construction compared to earlier editions.
From my experience 4e gives me well defined tools that provide more flexibility and better precision parameters to build/convert adventures and encounters. In 1e the base assumption was that monster levels/HD were used to determine challenge level. A monster of X HD was usually encountered in Level X of the dungeon. But there were little to no guidelines of what was "easy, challenging, hard, overpowering" to a group of adventurers, or how mixed encounters would play out. So a lot of the adventure/encounter design I did with 1e was ad-hoc and done by "gut-feel." Sometimes it worked out and many times I had to adjust on the fly.
When 3e came around it had solid quidelines for encounter design, and it had clearly defined assumptions of how the game mechanics were to be used to create combat challenges. A CR X monster was supposed to be a challenge (20% resource depletion) for a party of 4 level X characters. In that respect it was a better explained design. However the CR system left so much to be desired. It was time intensive to use, having to lookup stuff in tables, and it was horribly inaccurate. Some of the CRs were incredibly deceptive. The other problem was that monster advancement was a very time consuming process.
In this case the design system was more "precise" but it was not accurate - specially at mid to high level. Very few times did my encounters work right out of the box, and we still did not have any guidelines for rewarding non-combat encounters- except for one small paragraph in the DMG that basically boiled down to "make it up." But the "transparency" of the system was a step in the right direction.
4e kept the transparency of the design and greatly expanded it to make it easy and useful to the DM. The design assumptions were well communicated to the DM, and we got guidelines for creating, but more importantly rewarding non-combat encounters. Monster advancement was precise but very easy, harkening back to pre-3e design. We also got a much more solid framework for ad-hoc adjudication. In addition, the encounter design worked with the parts that it needed.
Don't get me wrong, not everything worked right out of the box, and not everything was explained very well. But there were more things that did work as designed than not. And thankfully those things that were not working properly, in a mechanical sense, were corrected through the errata process. Most of what I would consider "warts" at this point are not necessarily mechanical problems (except possibly Epic), but "errors" in presentation, expansion, and explanation.
I've gone long with the explanation of differences I've sees with the "tools", so I'll answer with more specifics of encounter/adventure design in a separate post.