Most of this show's obscurity is attributed to it being poorly advertised and being aired at increasingly sporadic and unusual times. The third season wasn't even aired until 2009, 4 years or so after it's completion in 2005.

As to why Nickelodeon did this could be attributed to it being a less conventional show by Nicktoon standards, I don't see any direct evidence of that being the case. My theory is that Nick gave shows like Danny Phantom and Drake & Josh were given priority given their creators seniority and better track records and MLaaTR ended up not having access to any good spots as a result. It's my opinion that Rob Renzetti's greatest weakness is his lack of seniority, MLaaTR is the only thing he created that had any noteworthy success whatsoever and he sort of flip-flopped between CN and Nick in between shows. Hartman and Schneider on the other hand stuck with Nick most of their careers, presumably giving them history and a positive reputation with the channel and it's executives while Renzetti would hypothetically be just another new guy in comparison. Renzetti's definitely has an amazing line-up of shows he's worked on, but MLaaTR's really all he has as a creator and that's probably all the station execs see.

Makes me imagine a nightmare scenario where the show lasts for a ton more seasons but eventually horribly drops in quality like Spongebob and FoP did. It's one of those details that usually makes me content with what a show I like gets, so long as it's not a plot-focused show anyway. Several seasons, a special and a ZONE flash is a pretty good run.

All in all, I do wish the show was more well known. It certainly deserves the attention, and is at least kept alive by old fans and artists.