Yes, replacing all windows but not the arched window. So you think it would be okay to do dark framed windows on the front of the house and white on the back?

Definitely. I'm a Realtor and have seen miscommunication happen between LL's and tenants over cosmetic changes. Verbal permission won't work if the property manager denies that you were given verbal permission. Have something in writing to protect you and your security deposit. Better if you can get it signed by the same person/entity that signed your lease. As to the flowers, check to see what is available in your area. I don't know which plants work there but a local nursery will be able to help you with the right flowers.

The house is pretty neutral, IMO, so what's your favorite color? I think the porch, sidewalk and drive are in need of an upgrade. Start with a cleanup of the porch. The step and walk should be as wide as the door itself, and the walk should lead straight to the street. The cracks in the drive can be filled, or you could add some interest there too with something entirely new like a grass and paver drive.

Here are some ideas. I know you didn't ask about this, but my sister had a cat-walk like you do that was open to the living room below. They built a floor and created a gameroom/bonus space. It was the least complicated thing they did to their house because they were also doing kitchens and bathrooms. The only little complication was that they had to raise the windows because they would have been far too low if they left them alone. It was a great improvement because of the bonus space, but it also made the living room below much more cozy and intimate. They were able to get rid of the 2-story hanging ceiling fan and install a beautiful light fixture instead in the living room. People actually use the living room more now than they used to. They didn't put doors on their bonus space but you certainly could. If you eliminate the lowest left-hand window in bedroom, you can install 30" custom closets that are reach in above and drawers below. If you get rid of the fireplace, you have more layout options. I put the long-hanging closet in the space where the bumpout and window are. It's true that windows in closets are not ideal bc the sun will ruin your clothes, but you could put a black-out blind on it. I put 2 options in this drawing, but it's such a large bathroom, you have a several viable options. I drew 2 that keep the toilet and shower plumbing in place. One of the options I drew would require moving the tub plumbing. Your bathroom is so large, you could have a linen/laundry cabinet in there in addition to tub, shower, vanity and toilet room. I love my linen and pull-out laundry. It's styled like a dining room hutch with a piece of countertop material and with the top portion stepped-back like a hutch would be. My cabinet builder made the pull-out laundry side look like drawers, to create symmetry, but they are fake drawers. I'm not a pro, so I'm sure others on here who are real pros will come up with better ideas.