Difficult to make suggestions without seeing a site plan with the house on it.

The foyer needs to be reworked. Perhaps have it parallel with the family room instead of being at an angle.

Master bath has some wasted space especially in front of the shower.

Agreed, the master bath is in need of a design rethink.

A couple of things I see. I feel you should revisit so that you create a plan that will address your near and long term needs. First, which direction does the house face? Depending on your station in life, and how long you plan to live in this house, you may want to cosider that the Owner's Suite is the room closest to the garage and the kitchen, and the bedrooms are located where the Owner's Suite and en-suite presently are. Your Garage is the most emphasized element of the front of your home, which I feel should be the nice covered porch, as it identifies and guides people to the entry itself.

My reason for mentioning the site orientation is this: specific areas of the home should be oriented in a certain direction, such that they receive the right natural light at the right time of day. It could be that the nexus of your plan is right, as shown. My concern is that to me, the top of the page usually depicts 'north'. If your view, per this plan is north and east, I think there are ways, even with the constraints of your site, as you say, that you could adjust this plan to better maximize the circulation and the natural light to the core of the home. I hope that this helps you in your design process. Happy Houzzing.

I am addressing only the master bathroom and safe. The tiny closet to the left of the master bedroom could be made double depth and the safe could go to the rear. This would be a natural way to hide it - the extra depth would hardly be noticeable. Your may need to move the bedroom door up a bit. This removes part of the long corridor in front of this closet. Even if you decide to put the safe in the master closet, it may still be worthwhile to make the tiny closet double depth to reduce that corridor length.

I am assuming you are not planning to gut the bathroom. I would turn the shower 90 degree counterclockwise and push it into the corner. I would put the tub where the toilet is now (remove wall of the toilet compartment). I would put the double vanity where the tub is now. Your double vanity as drawn is longer than the tub - that's huuuuge! I would choose a vanity that is about the width of the window. That leaves space on that wall for the toilet between the shower and the vanity.