The difference is that money wasn't Mr. Krabs's whole personality and that, along with the Camping Episode, it was funny.
SpongeBob's comedy rides a slippery slope where if you're going to do a cliched joke like Mr. Krabs's money lust or abusing Squidward, you have to literally exaggerate things to a point where they're so ridiculous that they're funny. The pre-movie seasons handle that ridiculousness well. If "The Camping Episode" was done now, the Post-Movie writers, no offense meant to them, would most likely have the episode mostly focused on SpongeBob and Patrick annoying Squidward in the tent and end with Squidward going crazy and running back home. That's not funny, that's just abusing a character. If you are going to abuse a character, go all the way, which is what "The Campinge Episode" did- SpongeBob and Patrick did a whole song, Squidward got mauled by a Sea Bear for no other reason than "it was funny", and against all odds, he failed at even making a tent.
That's so ridiculous that it's funny. It's the same with Eugene. Eugene going to such lengths to get 62 cents from the Dutchman- literally selling SpongeBob's soul- is so ridiculous and stupid on his part that it was funny, and even if it wasn't, Krabs apologized at the end, which was nice and rectified what he did. This is different from "Penny Foolish" because PF doesn't go as far as it needed to. Eugene makes a slideshow and a movie theater and stalks SpongeBob for a penny in PF, and that's relatively tame. And because nothing is so stupidly outlandish or funny in that episode, the comedy falls flat and people look at the character flaws Krabs presents in the episode. If Krabs had, say, made a dramatic short film, or even kidnapped SpongeBob (in a non-creepy way, of course) the episode would have been funny because of how ridiculous it was.
Eugene was always cheap. Just less so in Pre-Movie, but that's not even the problem. The problem now is that Mr. Krabs's money fetish isn't ridiculous anymore. It's just a tired joke that's swallowed up his character, and thus, it feels perfunctory, and because it's so tame, but at the same time, all he does, it feels more realistic. Add to the fact that money love and cheapness are two of, if not Mr. Krabs only traits that he portrays, non-outlandishly, in almost every episode, whereas Pre-Movie, he wasn't always cheap and when he was, it was so ridiculous it was funny? Yeah. It's definitely worse Post-Movie.
SpongeBob is an animated comedy. If things aren't pushed to their very limit at the right time, the comedy falls flat.
EDIT: oh, Safe Deposit Krabs is a terrific example of Mr. Krabs's money lust played insanely well. Having hallucinations with a money wife and a money dragon was great and totally out there, and something I'd like to see more of in the show.