I think a comfortable distance between the island and the counter is around 42". It seems that you have only 30" between your cook top and the counter. I might be a little too tight. The wall between the entrance and the kitchen could be 4' long instead of 6', you would then be able to move the island a foot which would give you more room between the cook top and the island. Could you switch the location of the toilet and vanity in your dad's bathroom so your enter facing a vanity instead of a toilet which is a lot nicer.

Leather sofas can really dominate the room and can give an overall cold feeling. I would add some earthy elements, like a wood coffee table with glass or metal. Go to Restoration Hardware's website and look at their sofa room scenes. And I'm sorry I think the art is too harsh for the room. That's all your eye goes to in the room. too overpowering. I would look for something softer or maybe a cool mirror and I would add color to the room with pillows and some colorful lamps. I also think woven blinds would look great. They add warmth and give a finished look. The color of your window treatments should contrast your wall color a bit, not match it or else it starts to look generic and blah.. You have warm walls, warm floors and the woven blinds, like Hunter Douglas brand would pull it all together for you.

The amazing thing is that you have the luxury of approaching the architect about these issues. Laminated glass should address the security along with any alarm or security system you plan on installing, though the laminated glass may have size limitations. Regarding the waterproofing you should contact the architect, contactor and waterproofing subcontractor, or see about hiring an independent waterproofing specialist who can detail and warranty the condition. As a design consideration, make the lower area a garden or gallery or sculpture area and upper should be all glass. Maybe a garden roof there too if accessible or visible. In any case looks like an amazing place!!

example: winding staircase, source internet Little modification need to be done for entrance lobby opening, where you could accommodate a shoe rack and the complementary vertical wall can act as a amazing entrance decor wall wall in Kerala style heavy color play or texture/wall cladding with brass mural.. by doing this you get space to mount TV unit and a good space for sofa arrangement (make sure sofas are light as the space is less to accommodate baggy sofas), staircase can be made in the shape shown in sketch plan, with marble finish on the foot steps (or as per interiors), space in the bottom of staircase next to master bedroom wall can be utilized for chest of drawers or a tall furniture, make sure the staircase bottom part to be casted smooth in finish.