If we replace them it would be just for aesthetics, the windows seem to be functional and water tight.   

Lots of newbies do best with lipstick flips where you're just doing some simple things like paint, flooring and general aesthetics.

Typically you are not deciding to use glass for thermal performance but for other reason like aesthetics. https://www.lowes.com/pd/SEVES-Glass-Block-Glass-Block-Common-8-in-H-x-8-in-W-x-4-in-D-Actual-7-75-in-H-x-7-75-in-W-x-3-875-in-D/1000095299This window is R-0 but I think the info is not provided here. https://www.lowes.com/pd/Project-Source-30001-Series-Tilting-Vinyl-Double-Pane-Double-Strength-Replacement-Basement-Hopper-Window-Rough-Opening-32-25-in-x-14-25-in-Actual-31-75-in-x-13-75-in/3683856This window is R-3.33   (U-value is reciprocal of the R-value)  1/0.3 = 3.33https://www.lowes.com/pd/ThermaStar-by-Pella-Vinyl-Double-Pane-Annealed-Replacement-Double-Hung-Window-Rough-Opening-27-75-in-x-45-75-in-Actual-27-5-in-x-45-5-in/3119077

I'd suggest attempting the simple aesthetic repairs yourself (drywall finishing, painting, staining, etc.) and save other work for the more experienced folks.

Over the cobblestone on the outside was a 1/2 inch thick facade that looked like a block foundation (purely aesthetic).

You might have a more aesthetically pleasing property than your neighbor but you are still in the D - same laws, same poor tenant base, same crime. 

It needs a some work:- new kitchen- aesthetics to bathrooms- new paint job** There could be more to it, but what i am getting at is how could one get this under contract at a fair price to either whole sale or fix and flip?

At most, as @Scott Mac said, drywall the vent for sake of aesthetics. 

When we purchase a property, we always look into what permits have been pulled in the past to better evaluate the value and integrity of the structure and it's surrounds.You wouldn't need permits for aesthetic elements such as: Cleaning, painting or refacing cabinetry.Replacing cabinet knobs and drawer pulls with simple, modern hardware.Installing new countertops on existing cabinets.Replacing backsplashes.Updating lighting fixtures.Updating plumbing fixtures.Replacing floor coverings.Painting over existing interior and exterior surfaces.

My personal favorite is porcelain tile as it's practically bulletproof and aesthetically acceptable here in Texas.