Arguably, the most challenging aspect of any story with multiple entries is delivering a "worthy" conclusion. I'm a big fan of games that explore sciency stuff, and when it comes to game (and movie) stories, I'm pretty easy to please. In spite of all that, I couldn't help but feel like the ending of Burial at Sea was Ken Levine aggressively expressing his contempt of his own fans. It's definitely possible that I'm taking it too personally and instead of expressing contempt for his fans, he was actually thumbing his nose at his former corporate overlords (I'm sure you'll recall he shuttered Irrational as soon as Burial at Sea Pt 2 went gold and started an indie studio). Regardless of his reasons, I found the ending to not only be disappointing, but offensively so. Your mileage may vary.
For what it's worth, I hope you enjoy it. At least then I can tell myself that it's a matter of taste, and I just don't appreciate the team's creative decisions. Until then I'm left feeling like I wouldn't piss on Levine if he were on fire.