Lots of great questions -
1) The slabs of PSA, SGC and Beckett are NOT the same size. They are generally pretty close in length and width, so storage for one generally fits storage for all, but if the holder has very little room, you will eventually run into trouble. Beckett is quite a bit thicker than the others, meaning you need more storage room.
2) Personal choice, but I bet most collectors like to see their cards "just so". I think they are much easier to access when they are all in one direction, upright, and of course, facing forward.
3) So long as the card itself is adequately protected, there's little need for felt or lined drawers. Its a nice touch, but not absolutely necessary. Keep in mind, you'll want to stack your cards so that there isn't tons of shifting room. Stack something (anything) in the rear portions of your unused drawers to minimize any sliding should something unusual occur. Once you do that, there should be minimal damage, if any, to the casings.
4) Completely dependent on your collection. Big enough to allow for growth, not so overwhelmingly large as to be useless wastes of space.
5) Something that polishes itself?
I'll add that I have something similar to what John posted in his second pic and love it. Its furniture and so it sits well within a normal room and it allows me to organize different collections and supplies in numerous ways.