Just an arbitrary thought... I'd like Thieves in Time to have an intricate storyline like Sly 2. Sly 3 wasn't bad by any means but it didn't capitalize on its potential. In retrospect, it would have been a great plot twist if Dr.M had revealed the home of the Cooper family to the Fiendish Five deriving from his envy of Sly's father. The time travel premise of Thieves in Time is extremely ripe with potential and I'd presume it's a genuine possibility both Clockwerk and Sly's father will be encountered.
I agree, I think it would be a missed oppotunity if those two characters did not appear.