Also, while both have had dealings with criminals and don't bother to play fair, Flintheart seems to be the more directly villainous of the two... I can't imagine Rockerduck stooping to attempted murder, for example, while Flintheart has done exactly that on several occasions.

That's pretty much the reason I like Rockerduck much better.

Scrooge and Rockerduck are rivals, but they also respect each other (Rockerduck outright states this a few times. Scrooge never admits it openly, but there was an old story where a couple of hired counselors forced Scrooge to stop fighting with Rockerduck because "it was a waste of time, better spent making money!", and Scrooge was incredibly depressed that he couldn't exchange blows with Rockerduck anymore), and occasionally even team-up for a common goal (I remember a story in particular, where they both hit their heads and lost their memory, and promptly became BFF). Their interactions can be actually fun, and have quite a bit of layers.

Flintheart may be an interesting character individually, as Scrooge's "dark side". But, from what I've seen, his interactions with scrooge as very simple, shallow and straightforward "I'm a bastard and I'm going to try and hurt you! MWHAHAHA!" It's just not my cup of tea.