In our unit we decided to go with a shower instead of a bathtub.

When I went for the inspection, and was able to walk through the units, I found that only about 1/2 the heat pumps were working, most of the toilets and bathtubs were leaking causing soft spots in the floors, there was fire damage in a couple of units that had been kinda covered up (wood paneling placed over the studs, but could see the charred studs because there were gaps at the edges), and as far as the new roof,When I brought up these items, they reply was, "well it's a C class property, what did you expect?" 

More than one bathroom makes a live in flip easier - you remodel one bath while still being able to use the other(s).A property with a utility sink makes it much easier to wash dishes than doing them in the bathtub, although your kitchen won't be torn apart forever.A garage to store tools is nice to have.Avoid the "weird" houses.

You need to give some more context so we can answer your question better.In my sub market, with the fix & flip deals I'm doing, the best value add for appreciation is putting in new flooring, baseboards, paint, cabinets, countertops, appliances, light fixtures, ceiling fans, plumbing fixtures, toilets, bath tubs, landscaping, windows, doors, electric panel, sewer, roof, and HVAC.

-Replaced appliances-Refinished cabinets and replaced tops-Refinished bathtubs and replaced vanities and toilets/mirrors-Replaced all lighting-Septic repair (replacing 2 damaged drain lines) What was the outcome?

In July 2012 my tenants reported that water was leaking in the kitchen from the bath tub above.  

There were only minor changes needed to turn the apartment to an office, For instance, an office does not need a bathtub, a stove, so these would have to be removed.He first approached the city and he was told what I was told, everything was to be ripped out, and put in again.

I'm going to assume that the OP was referring to painting the upper part of the dry wall as, many showers I've seen, not all, but some, do not heave the tiling or bath tub lining all the way up to the ceiling.

When I inspected the apartment it is in a very bad shape - carpets completely destroyed, several big holes on the wall, bathtub is all black, they unplugged the fridge and put food in there, so the whole fridge is molded. 

The bathtub surround is sort of warped so the seal is broken down near the tub.