Depends, did focusing on the change take away from improving other aspects of the game - coherent story, bugs, NPC development and so on....
Not really, no. Most of the work was on myself and programming, and I didn't spend the majority of my time working on it. The other designers were barely affected by any of the 2nd Ed./3E changeover stuff. As with any game, IWD2 had bugs, but the number and severity of bugs was pretty mild compared to the other IE games.
Most of the major flaws in IWD2 were developed during the first few months of the project, when we believed we were on a much shorter timeline. It was difficult to restore coherency or make other large course corrections later on. The 3E implementation was on a three-phase timeline that Malavon and I outlined early on. We never really knew if we were going to hit Phase 2 or 3, but luckily we did.
EDIT: A lot of the coherency issues came to light relatively late in the project, when we started doing extensive playthroughs. By that time, we could recognize that there were problems, but we didn't have time to overhaul the areas. For example, Targos and Shaengarne and the Ice Temple all feel very different and had many different problems during the course of development. It probably would have taken a long time to get those three areas to feel "right" and to better establish the story and characters in them.
Areas like the Fell Wood and Black Raven Monastery were the victims of vision exceeding grasp -- not because Dave made bad inherently bad designs, but because he kept running into engine and scripting limitations. There were aspects of the engine with which he was familiar on PS:T that were different in IWD2's code base, but he often didn't realize the difference until he had put a certain amount of time and effort into going down a particular path. He was disappointed with how he wound up having to implement those areas.