Actually you are a bit wrong here (on many counts)!
Exfoliated graphene from HOPG has, actually, phenomenal electronic properties. On the other hand for example, epitaxial graphene (sublimation of Si from SiC), which I work with, is typically less pristine than exfoliated (scotch tape method) due to either a buffer layer between the graphene and SiC (when grown on the Si-face) or a difficult to control and poorly understand growth morphology (when grown on the C-face). There are other details here that I omit for sake of the "layman's summary". More and more avenues of fabrication are being investigated/discovered/perfected as the years and months go on many of which produce graphene, but none of which produce as pristine graphene as the Scotch tape method.
Graphene on SiC is prepared by subliming silicon from the furnace in an inert ambient NOT chemically etching the Si away. It is highly controllable on the Si-face, less so on the C-face although progress is being made.
You say that exfoliation is not used any more to fabricate graphene. In fact it is one of the most common techniques. It is certainly not scalable to production levels but is consistent in producing PRISTINE and CHEAP graphene.
AFM will likely NOT be able to tell you the number of layers you have due to the exceedingly thin material. In fact, its even quite difficult to use TEM due to the highly destructive sample preparation process. There are several ways to identify layer thickness but many are contested. Some include, elipsometery, Raman spectroscopy, TEM, electrical measurements, ARPES, etc etc.
You may be right that the discovery "is not graphene," I think that the discovery is "realizing the usefulness of graphene." Moreover, de Heer emphasizes that graphene was known of before 2004, but it was not realized until, he says, his work in the 90's that such a material could be used for interesting/novel/high performance electronics. I think the Nobel Prize was given to recognize Novoselov and Geim's instrumentality in realizing this utility of the material, but maybe you are correct and that it should not be in recognition of "their discovery."