I have read Baka-Tsuki's translations of the light novels, so let's see if I can get the differences in the last episode:
In the novel:
1) Aria does not know about the weak spots, until Kinji tells her during the final battle.
2) Kinji fires the first shots, and demonstrates Vlad's regeneration.
3) Kinji frees Riko by stabbing Vlad with his knife, while Aria provides fire support.
4) The anime leaves out Aria's response to Vlad's genetic obsession, praising Riko's hard work at self-improvement. (Dammit, why leave out this, JC Staff!)
5) Riko never tells Kinji that Vlad's last weak point is in his chest; she knows that it is his tongue. (Why did JC Staff waste time with that mistaken attack?)
6) Riko does not pick up Aria during the flight, Kinji goes into HM from seeing her in her underwear.
7) During the final four shots, a lightning strike distracts Aria, and that is why Kinji uses Billiard Shot to correct her trajectory. Riko swoops in and nails Vlad in the tongue.
Left out of the anime (SPOILERS?)
The final bikini scene after the defeat of Vlad did not bring any sort of closure to this act in the story, and was too frivolous to serve as a finale. The cliffhanger from the LN would have been far better. I think JC Staff ran out of time to squeeze that in.
As far as JC Staff adaptations go, I think Hidan no Aria was more or less faithful, with the big exceptions being the busjacking and the final episode. Compared to ZnT or Merry, it's not all that bad, but the changes that they did make were really unnecessary, I don't know why they bothered.
Other thoughts:
Dammit, doesn't JC Staff have better music then using the OP during the final attack? Not that the OP is bad, I like that a lot, but really....
Overall 8/10. The adaptation was not
too bad despite the unnecessary changes, though my opinion of the source material is that it's really cheesy.