First off with the shower i'd recommend taking down the shower walls
if they are greenboard. Wonderboard (cement board) or hardiboard will
make a wonderful backer for the tiles. As for the showerpan, Home
Depot
really has crap. Plastic showerbases that are plain scary looking.
Home Expo (high end home depot) has fiberglass/acrylic shower
bases. They are MUCH better. Many local plumbing and bathroom stores
carry them too.

(Use the greenboard for the rest of the walls in the bathroom. Shower
walls
need something a bit better. I'd recommend using felt paper between
the shower
walls and the wood studs. Makes a nice water barrier)

As for tiles from Home Depot, that should be just fine. I purchased
mine
from them. Pretty good quality (I custom ordered a fish / sea shell
design)

As for the height of stuff, no real specifics. But i'd accomidate the
shower high
levels to all, not just you because you are tall.

Humm, for the nook for the shampoo its an either or kind of thing.
Its more work to do right and can be a source for leaks if not done
well.
But it can look nice if you take your time.

One thing i'd HIGHLY recommend is when at home depot, pick up
a cheap wet tile saw. This will make those cuts a breeze.
When you make the holes for the plumbing in the tiles, id recommend
using a rotozip (or equiv. device) to make the cuts. You can make
real simple professional looking holes very easily.