Pretty good.
The interactions between Wolverine and Angel in the finale made good use of Logan's backstory, though it also highlights the clash with the un-Wolverine-ish personality the show often writes him as (also, where were Beast and Storm in that extended fight? They just waited outside for no reason while Wolverine handled it by himself).
This was Storm as a character's most prominent role so far; used fairly well, though they might have spared one of the Wolverine solos in favour of giving her friendship/flirtation with Angel more time.
Warren Worthington II is a film import, but, as I thought in X3, he's a very good idea for the mythos. It adds something to Angel's character
Clancy Brown as Mister Sinister I found a lot better here than in his previous debut, but I think I like the TAS voice better; sounded weirder, as opposed to, well, Clancy Brown's standard villain voice. Sinister's visual presentation here likewise was a lot spookier than in #12.