Firstly, another thank you for taking the time to share your thoughts, the feedback really means a lot to me with this being the first game like this I've made. And secondly, yup you're probably right about the spoilers, but, hey, just to be safe: [MORE SPOILERS]
I entirely see where you're coming from, I had similar doubts! Tbh, I think I got carried away with wanting to pull off a hard-hitting bittersweet ending (always been a sucker for those), and conveying a sense of helplessness, and ended up not properly considering the impact on player agency as a result of that.
I intended to put in more interesting final scenes with Dr Laine at the end, but honestly I'd kinda run out of energy by then and decided to focus on streamlining and proofreading what I already had (with questionable success, haha), so I fully take on board what you say about the interactions with him not really mattering in the end. Once the Jam is over, I'd love to try and fix that, maybe add an epilogue. I really like your thoughts on having a 'hollow victory' with the Doctor being caught.
And yeah, actually, now that I think about it, I suppose having the option to rescue Sam doesn't necessarily negate the bittersweetness of the ending if the rest of Arbor is still destroyed, hm...
Yup, I think I might well come back and make changes after the judging's over!