Although there is no denying that Martian Manhunter is the best character and people may commonly complain about the character, when it comes to Grand Finals at a tournament he is not winning like pre-patch Superman was, and the match-ups actually look like a fight even if it is in MMHs favor.
One of the things that constantly surprises me about discussions like this is that people cannot accurately look at the facts. They will make a factual-sounding statement that is 100% false, without taking a little bit of time to just look at the results.
This is a perfect example. This statement is wrong. Pre-patch Superman was not dominant in terms of winning tournaments (assuming you aren't talking about locals, since Jupiter has obviously won his fair share). The only Superman who was winning sizeable tournaments was KDZ, and it's still not like he won every single big tournament he travelled to. He lost to Perfect Legend a couple of time, lost to Chris G, etc.
Despite being clearly the best of the Supermen during his run, it's not like KDZ setting foot at a tournament was a guaranteed win -- and he worked hard over a period of time to overcome some of the players and matchups that were giving him trouble. Not to mention that other Supermen hardly won anything outside of locals.
Jupiter has now won a regional, followed by two majors in a row. The only thing limiting him from winning more tournaments is probably the fact that he's young, in school, and doesn't travel much. But his win rate since hitting his stride is on par with any Kabal or Superman you can name.
In general, MMH was a DLC character, not a day-1 release character -- which is something Superman wasn't. Not only was he DLC, but he was close to the end of the DLC releases rather than the first ones. DLC characters always take much longer to hit their stride and aren't played at a high level by as many people (See: Kenshi/Skarlet in MK9 and how long it took them to hit full strength, maximize their effectiveness in matchups etc). So it makes absolute no sense to compare a late DLC character to a day-1 release.
And lastly, character dominance has never really been about winning every single tournament. Kenshi was a terror in MK9, and although he hardly won anything, he was a massive uphill battle for many characters in tournament play. Cyrax took over 2 years to start reliably winning majors. Even the Kabal's and Cyrax'es who didn't win were major stumbling blocks for a lot of players on their attempts to place. That's exactly what it looked like when Jupiter ran through the entire losers' bracket at CW without dropping a game.
So overall, it's hard to have a factual discussion when people don't look at the facts. Despite the fact that I think Jupiter is a great player and is making full use of everything his character has to offer, MMH is a problem that will only multiply with time and lab work. The story isn't finished yet; it's just beginning.