Congratulations on a beautiful home. Replacing the slate will lighten the feel and open your spaces dramatically. Consider a rounded matte terra cotta or limestone tile to complement the Spanish style of the home and the wood flooring you already have. Your walls have a good amount of texture so I would recommend a matte finish over glossy flooring for you. Taking a look at the glossy finish of the floors now, so much light bounces around, the floors attract attention. Less light bouncing about will help calm the spaces. I'd also recommend rectangular tiles for a more artistic feel. I've included some photos to get you thinking. The last two photos show what glossy terra cotta can look like - it's not my first choice for you. Best of luck! I'd love to see 'after' photos too!

also will give illusion of a bigger bathroom if you use bigger tiles ..I used small ones on one wall as feature wall and larger ones on other walls ..

It can either look really dramatic or too dark, depending on the size of the room as well as your other components. I've attached a couple of images of our work using dark tiles, the smaller bathroom we have surrounded the bath with dark tiles but then balance it with an extra large mirror to bounce the light around the room. The larger bathroom we have taken the floor colour way onto the wall but used a different texture on the walls for drama. Hopefully this gives you more of an idea but you shouldn't to nervous of the room being dark, it's where you can create a contrast as well as textures. Look forward to seeing what you go with in the end.

because the water could seep through the joints between the new tiles and sit between the two layers and affect the seal and also raise the height of the floor and affect the slope to the waste outlets..but, why do you want to retile if you're not using the bathroom??...for immediate resale consider bathroom wall to wall bathroom carpet, new wall paint, new vanity, taps and light fittings which should also be cheaper than tiling over the top and, if it's not allowed by the body corporate, it will be a risk to future sales as it should not satisfy a proper building inspection