I'm not a tiling professional but after we moved into our newly-built house we decided we didn't like the tile on the shower floor. We hired the same tile company who installed the original tile and they just put the new tile on the shower floor over the original tile. So the shower floor tile doesn't have to go under the wall tiles. Just be sure to caulk the joint well and check it often to keep water out.

The difference is more in the aesthetics. Whichever tile goes over the other will have the cut edge exposed. If the wall laps over the floor tile, then you wouldn't see the cut edge of the wall tile unless you laid your head down close to the shower floor. If the floor tile butts up to the wall, then you'll see the cut edge of the floor tile when you look at it from a standing position.

Now, if you caulk the joint that should minimize the visibility of the cut edges, but I'd still prefer the look of floor tile going underneath wall tile.

None of that is as important as the waterproofing under the tile. To have that successfuly done, the bottom several rows of wall tile will need to come up to be sure that everything will be done watertight.

Caulk after the fact doesn't do a thing except degrade and eventually let water in. You have to be sure that what's underneath won't let that water leak through. That's why thousands of "cosmetic" bathroom renovations turn into full guts. The shower areas werent' done correctly and have leaked to a much further extent than is visible while still covered with tile.

thanks for all the answers. now by caulking properly where wall and floor tile meet, do you mean i use caulk there instead of grout? i think shower pan is done properly, i had access to the site while it was built and saw water leak test that was required by building inspector. its just we did some changes to the bathrooms and wanted to change floor tile in shower to match overall bathroom design wise. great idea of my wife :)