The physics-based puzzles just bore me. They aren't hard to figure out or anything, it just takes time to put enough stuff where it's supposed to be and then you can go and continue to kill enemies. For me they just felt like an unnecessary obstacle to make the game seem longer than it actually is. Same with the driving sections.
I agree on both of those counts, particularly when such puzzles were re-used. The first driving section, with the boat skimmer thing, wasn't too bad in my opinion - although the mines svcked. But then that should have been it - getting a buggy later on felt redundant. I also don't think the driving section in Episode 2 added much to the experience.
I got to HL2 very late (last Novemeber) and I figured the gimmicky feeling of these was age - it's sort of good to know it wasn't just time taking the luster off of the physics engine.
Valve said it was a mistake to make the game episodic
Given Valve's already notorious reputation with release dates, at that time built on vaporware TF2 and HL2's weird delay, they should have known better. On the other hand I think the Episodes gave them a good opportunity to try new things and really focus on story developement.
It's too bad Valve isn't doing anything interesting at all right now. At least, nothing that interests me. I don't really care about DOTA 2 or Counter-Strike.
Nothing they've announced at least.