The person in the best position to guide you in your choice is your academic advisor and eventually students and colleagues in your laboratory. These people can save you a lot of time and help you avoid known obstacles and pitfalls. You still need to do some thinking about the suggestions you received. There are scores of resources in the form of directories or repositories on the Web to help you along the way. In particular you may want to read this one to start with : "Choosing your thesis and dissertation topic" at http://www.academicjoy.net/resourcesref-cire.html . Good luck.
Identify dilemmas depends on the quality and field of research ... You can split the article into a set of research questions and after you select this major problem ... I know I'm talking about generalities, but I ask you to clarify your question more so that an action plan.