I got the distinct feeling that when Don Paolo was in Curious Village and Pandora’s Box, the writers hadn’t come up with a backstory for him yet, so they just had him hint darkly about it. Then, by the time they had to reveal it, they had three other villains with their own linked back stories running around, and just sort of made a rushed one so Don Paolo could be involved in the time machine business too. 

Knowing that he’d been ejected from various scientific groups and organisations because his inventions and experiments were scaring people made me come up with all sorts of theories in my head as to how Layton might have crossed him.

Finding out he hated Layton, considered him his nemesis, took a personal interest in his cases and tried to kill him and his apprentice, all because Layon got the girl back in uni was the ultimate anticlimax, and it remains the thing I like the least about the entire series to this day.