Well the in-game designs were done in order to allude to a 2d in 3d design. I don't personally find them "cartoony" nor did I find the enviroments to be the same.

As for Brahne, I don't feel that comparing her to Golbez is right. She may start off the whole war nonsense but her role is pretty minor compared to the likes of Garland and Kuja within the storyline. As for designs, must I remind you of Borgen from FFII? He does not exactly come off as sinister or serious villain material when one looks at his designs.

The story is pretty dark actually, I think the lighthearted elements were placed in there to counter it. The plot and the way it explores it's theme of "The Meaning of Life" makes it one of the darkest games within the main series. I don't feel the characters are anymore cliche than previous installments and I feel they only help to tell the more serious parts of the story better.

The previous games always had light hearted moments thrown in to counter their rather dark stories. Only FFI and FFII are mostly serious but that is probably due to them being early installments in a genre that was just starting to grow within the video game media. FFVIII was also pretty damn serious as well with only a few humorous moments spread thinly through the game.

Overall, FFIX brought back good characters, better world design and a more interesting villain than what we got from FFVII and FFVIII. But that's just my opinion.