If Shulk is relegated to an AT, it just wouldn't look right. Think of the relationship between Monolith Soft and Nintendo, it's pretty clear they have a lot of respect for one another, and that they're extremely close. Monolith help assist EAD in developing major Nintendo titles, that speaks volumes of how integrated they are within the Nintendo infrastructure. I doubt a first-party developer like Monolith Soft, who were named "Nintendo's new first-party favourite" in ONM, are going to lose out. The company is going to be rep'd, and that character will be Shulk.
Who, in their right mind, greenlights a massive scale, open world RPG like X if not for the intent to capitalize and expand on the Xeno brand. People who don't think Shulk is likely can't see the forest for the trees, he just has too much going for him. It would also be a smart decision from a business perspective, one that Nintendo would only be gaining from. Not only is it exposure for Monolith Soft, it could also mean more sales for Nintendo. Monolith Soft/Takahashi is going to be making massive scale RPGs exclusively for Nintendo consoles from now and 'til forever so it just makes too much sense to rep them with a playable character.