How can I modify floors, walls, ceilings and furniture in a reversible way?
There really isn't a lot you can do to a floor which is affordable and reversable other than throw down a rug. A washable rug isn't unthinkable in a kitchen but personally I don't like that solution, not least due to concerns over trip hazard when carrying hot items. Serious burns are not fun (he says, having poured boiling water over his foot many years ago).

That kitchen floor is MUCH less offensive than many. I believe that, after living there a month or two, it'll just become "the way it is" and you'll stop noticing it except when specifically looking for things to object to. Meanwhile, putting a light-colored work table in the middle of the kitchen might change the look of the room enough to make you happier. 

Regarding the shower door... You may be able to dismount the doors and remount them upon departure, but the tracks will almost certainly need to stay in place. Personally I would STRONGLY recommend you talk to the landlord about this so he or she doesn't discover the change when you bring them to repair something; if they do approve this change they may also have opinions on where and how the doors should be stored. Again, though, I'd suggest you try living with it for a while and see how much it's really a problem rather than just being different.

Modifying walls: Hang art (up to and including quilts...); make sure it's properly supported per the complex's rules and be prepared to do some touch-up of the walls when you leave. And/or paint, with the owner's permission (again, they may insist it be repainted back to white when you leave). Or put up freestanding bookcases, or other furnishings to break up the wall.  (I once built a full-wall shelving-and-clothes-rails system for one apartment which was badly short of closet space. About $100 worth of white Melamine-covered fiberboard plus hardware. Backless, mostly freestanding, braced against the wall at each end of the room and with a few brackets anchoring it to studs to make it somewhat childproof. Much cheaper and more roomy than buying an armoire, not stylish but functional.)

Ceilings: If you're looking at the ceilings of a rental at any time except when in bed, you're probably looking too hard.

It's a rental. It will never be perfect. Settle for making it functional and comfortable. Your next apartment will have a whole new set of issues.