I loved the 'flashback' sequences. I found the puzzles way more obtuse in this. Some would say they're challenging, I would say, somewhat badly designed.
I'm not sure if you're talking about the flashback sequences (OK, there is more than one! Oops!) or the main game when you refer to the puzzles, but I'm glad I've seen a few people who feel this way (makes me feel I'm not totally crazy).
I came pretty close the other day to calling it quits on the game after a particularly annoying session — I had saved just after entering a challenge tomb... the tomb puzzle was largely "find the path up" and stumped me for a few minutes. Then, I got back on the main path and again hit a roadblock. I know what I'm supposed to do, but I also know I'm meant to get to a different vantage point. I'm just not sure exactly where. I don't really want white paint smeared everywhere in the world, but my plan is to revisit it tonight and turn the pathfinding assist up... I'm pretty fed up with not noticing handholds (or thinking I can grab onto something and then jumping to my death). I do like the fact the difficulty settings are customizable like that.
This isn't the kind of scenario that would be a total showstopper for me in general, but I am getting older, crustier and less patient... and unfortunately the stuff in between these moments hasn't been entertaining me the way the previous installments did. Of course, I'm one of those people who really enjoyed the first couple of new TR... so if it Shadow was just more combat and light platforming I'd have been pretty satisfied. Even though it sounds like it ends with a bit of a thud and it has never been the highlight of these new games, I would like to see where the story goes (and I think it's got some really great-looking moments... so I'd like to see what other artistry the team has come up with)
At any rate, I'll be giving it another go tonight, and if it still isn't clicking, I'll probably call it quits... maybe it's just not for me. Fortunately, if I do, I can trade it in for what I paid, so that's a plus.
(Also, agree with all the posts about the piranhas. Really, the swimming stuff in general is not my favorite... another annoying moment last night was coming up for air somehow turned me around at one point, and I wound up briefly going in circles.)