i had did that quest, except i didn't went to the cemetary after. Just did, and well done! I like the fact that Mathilda also have a line there (considering it could be Seen before having her). Would be fun if going back to the pawn shop would end in Geneva poorly trying to apologize. xD
To be honest though, I went to the cemetary once on arriving the city, and since there was nothing, i just supposed the story would bring me there at some point, if it wasn't for you telling me I could have completely missed that. Maybe you should add something in the pawn shop lady dialogue to hint the player to go to the cemetary after giving the Sword back.
On another note, after farming to buy everything i wanted before going to the outpost to show the captain letter, my characters were around lvl 18-19. Mathilda is lvl 10 when we free her from the prison, so you might want to find a way for her to be automatically adjusted to the average party level (if vxace have something for it)
(Edit a few hours later)
Also noted 2 gamebreaking bugs. If you go back to the prologue worldmap, you can't return in the main area worldmap, stuck in the fortress after the bridge where you met klari.
When you arrive on top of the temple from the feral beast's waystone, there's a small scene where you get lectured about not being on the temple roof. You forgot to bring back player control after the dialogue and therefore no key work, can't move or bring menu.