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. Excellently engineered with a lot of amazing new features, but a poorly written story and inconsistent characters. It's a bit sad, because I think this game has the potential to be up there with Insurgence, Reborn, and Rejuvenation, but it needs a LOT of polishing when it comes to the story and characters, and a lot of rebalancing in late-game battles.