I agree with some of your points here Jesse. I wish Uncharted did have some of this game's more open-ness and wave combat scenarios aren't fun in either. I do think this TR's combat suffers from more limited battlefields, so it doesn't always have more options than Uncharted does in it's mini-sandbox type arena fights where there are a ton of places to move around and ways to approach the combat. Weapon upgrades and abilities were another big success in this latest TR that Uncharted might indeed want to look at. I also loved Uncharted 2's early multiplayer before the patched it into a much less desirable setup, but TR's is certainly subpar. So I disagree with your last point to some extent.
Having said all that, ideally, these wouldn't be such comparable products. Uncharted was never a modern-gen update to TR like you mentioned. Their gameplay focuses were just too different and if it weren't for the similar treasure-hunting backdrop I doubt anyone would find them all that similar (pre-reboot of course). I hope TR learns a bit from its own series going forward. I wrote a blog on my wordpress about it recently. I think if they can combine the old aspects of this series with some of the new things the reboot brings we might have something much more special.That is obviously a whole other topic though.