Sure, certain slight plot holes begin to reveal themselves at that level of scrutiny. For instance, how does Mal get back inside after firing that cannon at the Reaver ship?
And it's just barely possible that a couple of scenes may begin to seem a bit slow in comparison to the meteoric pace of the rest of the movie. Mal's second fight with the Operative, and the "phone call" between Mal and Inara (though it's easy to just tune out and look at Nathan's pulchritude there).
But amazingly, what's good about the movie stays good, and gets stronger, and you realize that it's a handcrafted, one-of-a-kind item--imperfect, but with a patina and strength and purpose that make it more beautiful and valuable than the glittering, machine-made entertainment we're usually subjected to.
If the moment of Wash's death had only shock going for it, then it wouldn't continue to make my heart hammer after nine viewings. It's the extreme contrast of humor and violence, right on top of the extreme contrast of the crash landing with the red-lit, pseudo-peace that follows, that makes it so visceral.
The funny lines remain funny--though it gets more interesting to listen for audience reaction when you know what's coming. The biggest laugh has uniformly been at Kaylee's "twixt my nethers" line, though I have to say that Mal's "God! I can't know this!" reaction is almost funnier.
The great serious lines get greater. "Maybe that's why we lost," and "So here's us, on the raggedy edge," and Mal's whole speech in the dining room, and, oh my God, "He ain't comin'" and "Please God, make me a stone."
And the poetical, Jossy, Firefly-isms get more beautiful. "Not that to see you ain't--well, you look very fine," and "In earnest, Mal, why'd you take 'em back?" and "I'm a hairsbreadth from riddling you with holes," and "That was a piece of mercy."
Oh! And the little details you start to notice. Like Jayne's demon cup. I love Jayne's demon cup! That demon cup is an icon in the making.
And the fact that Jayne must've ripped the patch off the head-banged guard's t-shirt during the heist, because he's wearing it on his shirtsleeve in the Maidenhead. Sometime after cleaning up the Reaver mess in the cargo bay and having his harpooned leg stitched up by Simon, Jayne must've found time for a little sewin', and that's just all manner of adorable.
And the way the ship rattles and vibrates as Zoe and Mal discuss the man they left behind on Lilac, then the rattling stops and the daylight fades as Serenity leaves atmo, and suddenly Mal's all blue. Take me out to the black.
And the sheer damn unbelievable length of Nathan Fillion's eyelashes as Mal looks out at River and says, "I really don't." (Okay, nobody ever accused me of being consistently deep and thinky. I refrain here from talking about tight pants. But oh boy howdy, I could. A lot.)
And hey! It's Inara who shoots down the Reaver who cut Zoe's back open. (Many people objected to Amazon!Inara, but I'm not one of them. Who cares that there's no explanation for that outfit? It's hot. Maybe Morena Bacarin should play Wonder Woman. That girl's been working out--did you see her shoulders?)
And, holy crap--at the very end, Zoe's repairing the hole in the cockpit where the big stake came through. That's not symbolic or anything.
And did you love the way Mal turns his head aside just before he explains to River about love keeping a boat in the air, as if he's a little embarrassed to be saying such a sentimental thing?
I'm gonna be thinking and talking about this movie for a long time. Brace yourselves.