Talking about whether JM or an outside writer should have helped with the lyrics I think misses the point.
1. Think about the story. Not much really happens. Rebel town in evil empire without music. One guy is good at music. Bad guys show up to take a look. Princess falls in love with guy. Runs away. Prince blackmails singer's brother. Singer's brother decides to betray then doesn't. Prince gets pissed, kills brother. Accidently almost kills his sister. Loses his hearing. Because lots of people don't want the princes to die, she doesn't. The King decides he's been a huge asshole and lets the village have freedom.
If you want to do a more romantic story about good and evil, then have some sweeping battles. I'd listen to a Dream Theater song about a village fighting for its freedom. Or do a political intrigue story with more three dimensional characters and more intrigue. Perhaps even merge those two things.
I think the more fundamental issue is that the more romantic good vs. evil story is about the power of good to inspire strength against evil, and the more complex political intrigue story is about how humanity is moved by power and self-interest. I think JP wanted to write something about how the power of love conquers all. Yes love can be a motivating factor but I don't know what that amounts to without the will to make the hard decisions because they're the right ones. Topics that JP has written good lyrics about.
2. The tone. This is the biggest thing about TA that doesn't work that I read everyone talk about without actually saying it. Some of the songs on TA are corny, some are straight forward drama, some are very serious. Some of the songs are from a rock opera, some are from musicals, some are from more straight forward prog metal concept albums. It's not that these things can't be blended but this album ends up containing a lot of tone whiplash.
An easy example of this is to just look at the first three songs (Dystopian Overture, The Gift of Music, The Answer). All three sound like they're from different albums. DO is a combination of rock opera and standard prog metal instrumental. It's not "super duper serious" but it takes itself seriously/sincerely and moves through various dramatic themes. The Gift of Music is more straight forward prog rock, but then has the cheesy (and great!) "My Brother Gabriel" section that sounds like something from a fun Broadway show. The Answer sounds more like typical prog rock/musical music, and the lyrics/tone are actually kind of depressing because they present a character who's so isolated from any traditional sense of humanity.