No. It's fundamental flaw was it didn't know what its audience was. It's the old fable about the Father, Son, and the Donkey. You can't make a film for children, teens, and adults; you probably need to pick two, at max.
I enjoyed the movie immensely, almost as much as I do Atlantis and Treasure Planet, but the fact is that at the time all three of those movies came out, animation was still considered as being for children. Not by audiences, but by Hollywood. So that meant that there had to be compromises during production.
No R rating, or you don't get funded. Wacky comic relief characters 'for kids' that any child would consider annoying and useless. Marketing on children's programming, and toy deals at McDonalds. It's those things that signal to mature audiences that an animated film is 'for children'.
We've had animation made for adult audiences before. 'Wizards', for example, and 'Rock and Rule'. Those chose an audience and stuck with it, and were never involved in toy deals or other such child-oriented marketing. However even with South Park, which was contemporary with Titan AE, also suffered from major criticism for being an animated program that was 'too adult' and somehow corrupting the youth. But adult audiences knew South Park was not for children (even if children enjoyed watching it), that's Hollywood and the media complaining about someone breaking the stereotype.
And that's all it ever is. It's always Hollywood know-it-alls or media pundits that label shit incorrectly or force it to be something it shouldn't be, causing it to fail.
Titan AE didn't need to be Saving Private Ryan, but it did need to understand it was a dark story about human genocide that might sell better to teens than to goddamn 12 year olds.