Great read! I'm wrapping up tomb raider myself and I have had the same feelings as you. I agree the story is a little weak but i was getting hung up on all the comparing to the uncharted series because tomb raider is great in all the ways uncharted is not but tomb raider does not out uncharted uncharted. Also not living up to the tomb raiding part of tomb raider kinda bummed me out that all the optional tombs are just puzzle rooms.
I also feel the emotional struggle of Lara dealing with the wild of the jungle fell a little flat to me. All the emotional set pieces quickly fade once the set piece is over and does not have any lasting impact. All an all its a great game and loved the use of environments and mood that the game sets up.