What you are missing is tons, absolutely tons, of hard work. Being asked to join a lab on a PhD project is flattering. Other side of the coin is that the prof needs, absolutely needs, people to do a lot of heavy lifting.
Good grades is one set of qualifications. Stamina to complete on time is equally important. With 2.5 GPA it might be that stamina is what got his attention.
Mind you doing a PhD is no bad thing. It just isn't that glamorous.
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