The stakeholder(s) are those who are affected by the success or failure of the application. Users are stakeholders; if the application succeeds, then it will add value to their lives (and vice versa; if it adds value to their lives, it will likely succeed).
But there are other stakeholders. The project team are stakeholders. The investors are stakeholders.
The user is unlikely to be the main stakeholder, because the user doesn't generally influence development until after the application is fielded. My mind can't quite wrap around the question of the stakeholders choosing the software methodologies. Reminds me of the "Camel is a horse designed by committee" quote. I think the norm would be that the software development team would choose the software methodology (constrained by what the company can license, and similar external factors).