Armed with the power of a legendary Trident from another world, a soft-spoken teen must battle against the wrath of an aquatic alien species as well as that of his best friend, all who whom seek the Trident for their own purposes.

Story began in 2003 finished at the end of that school year in 2004. So yes, I already had this before I had even heard of Percy Jackson (I didn't know about the book until 2007 and didn't even become interested in it until 2013). I disagree with you, but I can see what you mean.

You are telling us that you wrote that story 9 years! Because the book was published July 2005.
You may disagree, but from your logline your story is eerily similar to Percy Jackson and the lightning thief.
Young soft spoken boy discovers a secret weapon. That weapon belongs to powerful beings. It is then stolen by arch nemesis who had initially pretend to befriend the hero.

>>If the protag has the trident, the conflict is all about him retaining it. That will end up reactive, static, predictable. Give him a goal that sends him on a journey.

Agree. The Trident is a MacGuffin, the organizing principle of the plot, the object everyone wants.

>>"all who whom seek the Trident for their own purposes."

Okay, they seek it for different ends -- but they should be using the same means, that is, by exploiting whatever special power the Trident has.

>>"Though the Trident has many abilities"

I think it might be better to focus on one feature. The ark of the covenant in "Raiders of the Lost Ark" is not a multipurpose, supernatural Swiss army knife. It does one thing well; it has one unique feature that the Nazis covet: it makes the army that possesses the ark invincible.