Did you read the article you linked? The article was against retiring the VSEPR model:
"Critical analysis, which includes a detailed examination of the photoelectron spectrum of methane, reveals these premises (premises on which the anti VSEPR advocates established) to be ill founded and inconsistent with modern electronic structure analyses. Placed in a modern context, the hybrid orbital concept helps to familiarize students with the methods of working chemists, foster construction of a deeper, more interconnected understanding of chemistry and its connection to the laws of nature, and provides a secure foundation for more advanced chemistry classes."

I do agree that VSEPR is a good model to be used for into chemistry classes. There are even exceptions to some molecule structures within VSEPR theory itself, for example The gas phase structures of the triatomic halides, AX2E2 molecules which are linear rather than bent, and AX6E1 molecules, which are octahedra rather than pentagonal pyramids. So the theory does recognize that there are exceptions to the rules. I wouldn't say that just because in advanced and specific cases that the theory should be done away with!
My university has an AFM lab! But it is only open to graduate students and really only works with very specific cases.