Hmmn, let me take a crack at this.
I think the simplest reason to make a new system rather than relying on D20 or the OGL is when you need your system to do something that is genuinely different than what you see in a D20/OGL game. That's about the only reason.
Is there any reason that Serenity wasn't released as an OGL game? What mechanics of the Firefly TV show or the Serenity movie couldn't you accomplish with D20/OGL? To my mind, none. Would a D20/OGL Serenity game have sold better? I would say yes, largely because almost no one is buying Serenity for its game system. Having played a Serenity game, I can give my opinion that it is one of the worst commercial game systems that has come out in the last several years. Nice looking book, though.
A friend and I have made a habit of stopping by new game companies at Gen Con and listening to their pitch. If their game is basically a stat + skill + die roll game, with class-like and feat-like objects, we ask them why they didn't release the game as either D20 or OGL. Sometimes they have great answers (ask this question of Luke Crane, author of Burning Wheel, and you'll get some free entertainment) but oftentimes the answers we get show that the person doesn't really understand the difference between D20 and the OGL or really hasn't even considered the idea.
Should Iron Kingdoms go to a different game system? Only if there is a reason for it, and the designers can't get something important to work as they like using D20 or the OGL. From where I'm standing, I don't think that there's anything about the setting that couldn't be done well if the designers understood the OGL (which would be the only real option for a solid Iron Kingdoms game in my opinion, the D20 license doesn't really suit it).
Creating an OGL Iron Kingdoms game in the lackluster way that Deadlands D20 was born, on the other hand, should be avoided. If you as an author don't like the system and haven't taken the time to really play and learn it, you shouldn't build a game around it
So those are just my $.02 on the matter...
--Steve