The topography and history are closer to Baltimore than Indy? It's historically been part of the Rust Belt. It's considered part of the Great Lakes Megalopolis [0]. It's on the Western side of the Appalachian divide. Culturally it has far more in common with Cleveland or Columbus than Philly or NYC. The only reason it's even a question is because its in Pennsylvania, which contains Philly which is clearly East Coast. But cultural, geographic, and economic regions aren't defined by stat borders. If instead of being a part of Pennsylvania, there was a "Western Pennsylvania" and "Eastern Pennsylvania", no one would question lumping Western Pennsylvania in with the rest of the Midwest.
A good read, or you can come ask the locals what they think - be prepared for a big argument :).
From your link "Map of the emerging American-Canadian megaregions as defined by America 2050."
Emerging - not historical.
Pittsburgh is not 100% midwest. We are not like Nebraska, at all. The further you go from Pittsburgh the divide grows starker. There is some in common with some great lakes rust belt cities. That's it. In any case, it's not 100%.
Not northeastern != midwest. Pittsburgh has far more in-common with Baltimore than it does Indy.