I enjoyed this retrospective, though I think that the PoP story was actually more planned out than most people give it credit for. The 2nd game was dark, yes, but it was supposed to be-the Empire Strikes Back of the series, basically- and while the feel was disjointed from the first game, (and they didn't give nearly enough backstory for it, in my opinion) it fit in the overall picture, which couldn't be understood at the time; the 3rd game wasn't out yet.
The REAL issue with the 2nd game was that there were glitches in that fucker that could prevent you from completing it, and that is damn near unforgivable. In addition, you had to find all the fucking hidden extra health/sand capsules to complete the game, and making 'bonuses' the only way to actually have enough endurance to fight the final boss is bad cheese, baby.
Plus they removed my favorite part of combat; the Flash hyperspeed moments! It was the only cool thing about the combat from PoP1.
Finally, they decided to place the emphasis on the enemies as your enemy, instead of your actual opponent throughout the game; the environment itself. Think about it; who wants to kill you more; the room you're in, or that random shadowy piece of crap you dispatch with your sword?
There still needed to be work on the combat aspects of the game, especially in the 3rd one, but the storyline was compelling...even as it fell to a few cliches. However, the focus on the environment as your opponent returned, and the combat was the same as the 2nd game (meaning, improved but you still did the same 2 motions for every hard boss: Leap, slow time, grab-stab jump away) so it's not like that involved skill, but it didn't matter; the storyline took the threads going back to the first game and tied them together as well as they could.
If anything, the series suffers from Matrix syndrome, where if they'd been able to realize all three games in one shot then it might've flowed a lot better, but at the end of PoP1 it's done, you're over and there doesn't need to be anything else. Since they could only do the first game, giving a Halo 2 style ending was out of the question (probably a mixed blessing)