Not many options to upgrading windows without removing them. You could add grids, but they're not particularly attractive on a brick home, and the inside shutters would detract from the look.
The upper deck isn't ugly, and it adds value to the home so I wouldn't lose it. The problem overall is too much white. All the posts and any paintable trim around the windows and doors could be painted in the green, leaving only the spindles on the main porch in white. Paint the second story door green (assuming the front door isn't green). A stained glass piece in the transom would look sharp.

I just had all my windows replaced with high-grade vinyl framed, double-paned, completely screened, installed, guaranteed-for-life windows. Made to measure for my house. Highly affordable. If I had used wood-framed windows, it would have cost me a lot more than $550/window and I would not have gotten windows to fit the current. In fact, I was not happy with the inside trim work on 3 windows, so the company sent someone back to fix the problem. I was very satisfied w/quality work and solution. (I have 50-yr old ranch. The trick is not to accept their 1st two prices!)

As for the balcony, if you remove the railing, but keep the portico (well, it is the porch roof!), and have the window changed to look consistent with the other windows, it would sovle the problem and definitely give the entrance a classier look.

It's just unfortunate that today's building materials don't do justice when it comes to maintaining this type of architecture. I suppose the fascia board could be made wider instead of the stepped appearance, and of course color choices could be different, but there's nothing ugly or unclassy about the balcony! The brick will always look like a repair job if the door is done away with.

And as inkwitch says, fine restoration is really cost prohibitive for most of us.

Upper deck looks fine - topnotch in fact! What is the concern about it? I agree for most buyers this adds a lot of value and charm. Great place to drink morning coffee.