I also find the floor plan cramped and not exactly modern. But since you have a lot of space, you can afford to "clutter" it. If you like it that way...
What I really don't like is the master bathroom upstairs with the only access through the bedroom. In the requirements description, I read something about a playroom; so the mentioned son is still at a playing age. Little ones quite like to share the bathroom with their parents. That means: the son always has to walk through your bedroom. Personally, I wouldn't want to put up with that.
Overall: you have a lot of space and I'm sure there are much smarter ways to plan a house with a granny flat. Especially considering that the son is obviously still in playing age and doesn't yet need a very separate living area.
Without having a floor plan in mind: wouldn't it make more sense to plan a comfortable guest area in your half of the house, which is initially a children's area, i.e. a large room with a separate bathroom, fully integrated into your house? You can still plan a granny flat, but initially leave it in shell condition and use another room in the basement as a guest room. When the son is old enough to move into his own area (before he leaves the parental home completely; which never has to happen if he gets such a comfortable apartment; so I would consider that...), you can expand it as he likes. Until then, tastes and preferences will surely change. Or you use the granny flat as what it is: a rentable granny flat until the son is old enough to move in. So make a fixed-term rental agreement immediately. Advantage: it generates income that can be well used for financing. I don’t know how your apartment situation is; here in the Munich suburbs, you don’t have to worry that the granny flat will remain empty, you can rent it out immediately even with a fixed-term lease.
And: looks like it's self-designed. Right? For a house of this size and with the various requirements, I would definitely look for a good architect. The 5,000€ is certainly well spent.