So I'm playing through it right now and just wanted to add my thoughts. Gameplay wise it's one of the best fangames I've played, up there with Insurgence. There are so many new features added that it's hard not to appreciate the game. There's fusion, actual boss battles (with huge HP bars and no status effects), collectible trading cards that buff your team, new types, levels over 100, and more.
But like you said, I think the main weakness of the game is in the writing. I'll try to be light on spoilers here.
TL;DR I'd give it a 7/10. 9/10 if you ignore the story. Exc