I found the listing online via GIS, and I'm wondering if this was a MIL or illegal apartment at some point, which didn't help matters. My guess, given the styling of both kitchens, is that although it is plywood, it's still of the time, and thus better than putting in modern builder grade chipboard based veneered cabinetry. I would try to use some of what is upstairs to help the reno downstairs if you can't find something at your local habitat reno store instead if you're going to keep the nicer ones painted anyway--just paint them to match, swap pulls too.
Now where safety is a concern, like the faucets, that's a different issue. Sinks can be re-enameled and modernized as JRC and CS suggested. I know you don't like the open look beneath, but others do. It may also be cheaper to re-enamel and find the towel railings that are appropriate to such styles than an entirely new sink + cabinet. You could possibly do a beadboard style undersink cabinet, scoring the beadboard to wrap to fit the curve if you have the skill. You'll have to go with one smaller model anyhoo, because of how tight the egress seems from the door in the half. It might be worth pricing out options before you dismiss those suggestions.
I'd recommend wearing a mask when working on some of those floors--could be asbestos tiles which from my understanding may also have asbestos in the glue. Most flippers poly sheet and plywood over them before adding new flooring, which can be a pain dealing with how it offsets room change rises, trim, cabinets toekicks, doors (and thus why trim starts to vanish because they mauled it during removal).
It is odd to not have the mirror window on the other side of the fireplace, but it may have been later removed for whatever reason. I can't see evidence of such on the brick outside from the pics, though.
Regarding the lack of built ins, it's a '28 build so the original owners may have had all their older cabinetry/wardrobes, so they thought it impractical to replace what they already had. It's also possible that whomever tried to upgrade the furnace ducts to current code HVAC ripped out some. There could have been wood boring insect damage, or the cabinetry may have been asbestos--"fireproof" asbestos fiberboard built in cabinetry was also a thing back then, which I only found out about recently during my research about craftsman homes.
What is in the basement that looks like either wood storms or possibly the original windows that were removed? I can't quite tell because they're on the far side of the furnace.
I understand your frustration with which direction to go for windows, as well as your view that if you don't replace one or the other, it's half done work. For us, as we looked at homes this year, we outright dismissed all homes that had just solely vinyl, and didn't immediately dismiss (even bid on) a mix of vinyl and wood. It drove us crazy to see all the old homes for sale here where the listing boasted of upgraded windows. I know we are not average in that respect, but I want to mention it for the sake of the discussion at hand.
I know your old house loving side is fighting your knowledge as a realtor. However...if folks like us do not educate the buyers and the public in general, they will always believe what marketing folks tell them. Educate the buyers about the long term benefits of original wood windows, as opposed to the cost of having to replace vinyl within a relatively short time span, for instance, which means they often don't reap the promoted benefits before they have to be replaced. (Have copies of one of the many articles written on such in your buyer handouts. Here's just one:
http://www.parks.ca.gov/pages/1054/files/heritage%20canada.pdf) I know there are many buyers who are blinded by marketing, but we don't have to accept that fact--sometimes minds can be changed.
You may not be aware, but there's even talk in some building circles now about how vinyl windows and siding may not too far in the near future be considered on the same tier as asbestos products given the off gassing, particularly during fires. There's also the issue of how soon the double glazing fails and lack of ability to be repaired even on mid priced ranged windows. I just noticed re-reading the thread that Kashka-Kat hit on this too.
If I were you, I'd spend the money you were going to spend on replacement windows on a better (period look) front door and screen/storm--and fixing the ones you say need it.
It's clear that exterior work in particular is a race against the clock weather wise given the lakes area it is in, which is affecting some choices before the home goes back to market.
I would recommend not painting anything black, and instead use a deep pine/hunter or even a navy based grey to contrast with the warm brick. You could also use a third paint color matching your brick one some details, depending on how much there is to work with. This would give you the white, warm brick and then your wood color for three total. An off white would be better, but you've already noted why you are compromising there. That way if the future owners want to work with that in their scheme when they repaint the home, that will be less they will most likely have to do. For the green or navy gray accent you choose, I would also use it on the column details.
I think part of what is bugging you for the exterior is the lack of trim on all that trellis--both for the vertical plants and in the basement windows. The open ended look gives an unfinished appearance It also doesn't help that where they inserted the trellis over plywood, they didn't paint the ply darker for contrast.
This also goes for hidden/missing trim on windows--when the aluminum storms were added--and the doors. I see you're missing some (even for brick faced buildings: source:
http://www.oldhouseguy.com/window-designs/ ).
I know darker roofing is preferred in that area, so have you considered the nice dark greens available? You may have been thinking of the charcoal given the black details, but it's just too stark with the white. Too stark for the period, really.
Overall, I honestly don't think you should ever call yourself a flipper. You've obviously put a lot of thought into being as true as you can without the usual flip cheats. If I were you, I would promote this as a thoughtfully restored home.