They can't make things too complicated or the young audience will have no idea what its about.
It's easy to assume that kids wouldn't understand a more complex or darker plot. But instead of trying to go on a whole tangent about why kids are underestimated, I'm just gonna give you two words of advice. Watch SatAM. It's sheer proof that decent plots don't faze younger audiences. No... Just watch Avatar. That's proof enough (even though Aang's made some dumb decisions in my opinion, and I'll admit that). Trust me, kids are alot more intelligent than people give them credit for.
Deviating from the games is a step in the right direction. But they really need to drop this stupid League concept. Once is alright. Twice is... ok. Three times is... too much. Four times is just plain redundant. That's one of the main reasons so many FanFic writers and critics hate Trainer Fics. They always seem to focus on the League, and it's boring.
They don't have to deviate totally from the games. They could have the same towns, the same Regions, and the same evil Teams.
But above everything else, they should focus on coming up with a real villain. And I don't mean Paul. Paul's a good antagonist and he's a great rival, yes. But he's not villain material. They need a good villain that can actually put the heroes, cities or Pokemon in real danger, while maintaining their antagonistic standing beyond a mere two or three episodes. In other words, an entire season or story arc using this as the central focus. And it needs to be someone that can actually measure up to even Legendary Pokemon. Maybe this villain could even be a Pokemon (though that's not necessarily required). THAT would make a good plot.
And one more thing. I don't think it's necessary to change the main character. Becuase even Ash has proven that he can adjust to the situation at hand. And if things became more serious and the world was in danger, we'd see his character make adjustments just the same as anyone else. So it would still work.
I hate using Dragonball as an example, but it sort of fits here. Remember how Goku was in the first two seasons of Dragonball, before King Piccolo killed Krillin? He was cute and carefree, but he still wanted to be the best. After Piccolo killed Krillin, his composure was gone and he got way more serious. The point is, Ash and the gang are capable of the same emotions, with the proper motivation. I'm not saying kill anyone, because there are plenty of other ways to get their composure to change. Going back to SatAM, the characters in that were serious when they needed to be, but they still got a laugh out of the audience from time to time. I'm just saying it's possible. It can be done.