The common consultant answer is "It depends on the situation"

Let me take Three major agile methodologies XP, SCRUM and RUP and describe a rational approach to choosing a methodology.

To begin with let me define the parameters:

Agility: How quickly can you decide? How often do you release?

Technical complexity: How innovative is the solution domain? How familiar is the team with technology stack?

1. For situations with less complex technology and an organization wanting to start quickly, getting an XP team and business owner in a room will be effective.
2. For situations with high degree of technical complexity, it will be helpful to address architectural issues through an Elaboration phase, before embarking on fullscale implementation. The RUP model also helps very waterfall organizations to transition to agile because Inception-elaboration-construction-transition roughly maps to define-design-build-verify)
3. For situation with medium complexity and organizations new to agile, SCRUM provides a basic framework to empirically, but decisively work towards the product goals

But there are several other reasons why organizations choose one method over the other. One of the most common being: We have used it before.