Possible new layout. Tub is more than likely going in front of window where it says shower.

Obviously depending on the overall look that you are going for will dictate the final design. However for a timeless look in the colors your have described a 1" hex marble floor and a 3 x 6 white subway tile would give the timeless look. We have used those tiles for 60+ years and they are still in fashion today. I would use some Glass tile to give the space some pop but be mindful of trendy colors that may be hard to decorate around in the future. Remember avocado green was a cool appliance color once.

Great material choices. The vanity could be painted a gray color to compliment the other tones in the finished.

I actually really like the weathered wood vanity, and although I can't tell exactly what the top is, there is no reason it would not go with white tile. I like the idea of subway tile -- it is timeless and blend with many other things. You might want to rethink the black shower floor, however. The pebbles feel good on the feet, but depending on the water in your area, mineral content could make the black hard to keep really spotlessly clean looking. A pebble mix that would blend with the countertop might be nice, and more natural-looking. Also, you might consider just a simple "swizzle stick" tile line to break up the white of the shower, rather than glass tile. It could be a really sophisticated look, and a color to coordinate with the vanity top would be great. Then, if it's brown or dark green, or charcoal, you could use that color for towels and accents. As for flooring, a beige/grey limestone would be perfect with everything else.
Good luck.

Dont forget the recessed cans before they close up the drywall...maybe a heated floor. I agree that your tile and flooring choices should be variations of weathered stone colors. Your weathered cabinet is such an outstanding piece. Outfit it with the perfect faucet/mirror and sconces, and it will be a beautiful focal wall. A chandelier over the tub would be a nice touch..if code permits.

Here is the view completely gutted. Freestanding tub will go in front of the window. Shower to the left of that. Toilet to the right. Found a crazy white wall tile that they call gator. Not going to use it for fear of cleaning issues. But I thought it was cool. Definitely not timeless though. My dream is to never renovate this bathroom again. I like the subway tile idea but I am thinking 10x16 or 12x24 white staggered horizontally like a traditional subway tile look. Less grout.

Gator tile

You don't neccesarily have to fear grout as it can add style to the look. A good sealer will last a couple of years and is easy to apply. I have used the 12 x 24 white tiles in a few jobs. ( my own house as well )they are nice but do tend to feel more contemporary than traditional. The epoxy grout is a great recommendation. I would probably go with the brick pattern if you use the large tiles tends to look less grid like. Sounds like your on the right track. Good luck.

Almost done just waiting for the glass and tile guy to come back and finish the shower. It was a rough road and had a lot of problems with the contractor. But for the most part my vision came to life. Couldn't get the vanity I fell in love with because they sold out and I would have waited a few more months to get it. But I think what I found worked out great.

More pics.

Great job Maggie the project looks great! Sorry to hear about the problems with your contractor. That does happen from time to time I'm afraid but the bathroom is superb.

Looks great! Love the paint color!