One thing I didn't buy in the film was Mr. Universe's planet - how do you run a broadcast/relay station on a world surrounded by a plasma cloud?
I also didn't like "mean Mal." I know the way he is in the film is the way Joss wanted to portray him, but the Mal of the series was the one thing Fox's notes got right.
Good point, when I saw it I did think Wrath of Khan and Joss confirms that on the commentary. But maybe he used the planets interference to hide and had some way of getting through the static (a short range relay satellite?)
I think we get nice Mal back at the end but like S5 Angel or S7 Buffy he's in a hard place and must be a hard taskmaster.
The Mr Universe married to Saffron idea is inspired
although it would have negated the Buffybot spilling the secret concept. If you find/write it let me know