Both the Shin Megami Tensei games and the Persona games are very heavy on player choice. It's an incredibly important part of both the stories and the gameplay. Heck, Persona would suffer more for having dialogue options removed than Mass Effect would.

Is the story more scripted? Honestly, I don't think so. You still have just as many options in side quests and content that isn't part of the main story. Your decisions still change the people you interact with, how they relate to you or their own problems, and the main stories of both are beyond your input except for a couple of key decisions.

Even if it were more scripted, so what? It's still interactive storytelling. Go play Golden Sun (seriously, do so, it's a brilliant game). That's a linear story without player choice. Look at how few options you get, and look at how many of them require you to choose a particular answer in order to proceed, or steal your answer away if you don't make the one the game wants.

Persona is a game based on choice. The entire Social Link system is driven by choice. One of the biggest themes of the story is choosing the path of your life in the face of a looming fate. The choices you make determine the course of your story. That is why they are there.