I believe the negative flipside of Agile, is that though the positives of rapid development, creativity are core to the methodology, the other core principle that that the customer/client (be it internal or external) can be lost in that environment. In such situations more traditional process, and communication can salvage the project, without damaging the overall Agile process.
As with most new methodologies, there is mistaken assumption that by simply adopting the methdology in development will somehow work. I reality, all project members have to be working not only to same guidelines, but also not to forget that each project member represents his/her own project area. Project Management and QA are usually the common areas of failure in Agile environments, which of course leads to damage to relationships external to a company.
There are tools specific to Agile, and MSProject is not my first choice as a project management tool in any case. I always found dotproject was a better integrated project/QA management tool, which is more suited to rapidly evolving Agile projects. However the core of Agile principles is more to do with a way of doing things, rather than software enabling this to happen.
Nothing new has really been introduced, as the idea of development and testing working closely together is just sound software development practice, and shorter release cycles is more appropriate the demands of modern software projects. What is new is better accountability of development, and more interactivity between a company and their client. i.e. more transparency generally in the project lifecycle.
This information was based on my own experience, and in media/gaming way, QA has always been more of a challenge, due to the creative and emotional level of people that work in these industries. Automation is heavily featured in Agile methodology, but in my experience the biggest challenge with Agile is people, not technology.