Wow this is an incredible coincidence. I happened to just finish the third Amulet book today so I know exactly what you're talking about. I can't really see a similarity between Ganondorf and Lugor myself but I getcha. I love Trellis!
Just think about it, Luger and Ganondorf are evil, they both wield powers, one sword, transform, and have armor. Do you own book two? if you do look back, and take a good look at Luger, and then Ganondorf. Just give yourself sometime to think about it.
I guess I find it harder to see the comparison with their faces and hair being so different but Lugor's armoured bulkiness does remind me of Ganondorf. I only own book 1, books 2 and 3 and library books.
Jeez I only own 2, and 3, due to the fact that my younger cousin had to give me his twenty which I gave to the shopkeeper. Have you seen my fan series Amulet: the new frontier? if you haven't click on my username, and see I just finished page four. But that derpy face Ganon had; it made me laugh.