I do have an idea, but I'm really surprised how no one else thought about it exactly in my way...
But before I speak about my thoughts on this, I want to say something else - no matter how much a person is lost in his research, they will come home, at least at night. By rarely, his wife must mean that he comes back late at night, and leaves early in the morning. But he must come home to sleep.
Now, to my point:
The upper floor could be just a room full of books, or a new plot-device to support a deeper plot, or it could be... and egg research room with different eggs and computers, from the idea that someone else mentioned.
I think the idea of it being an additional scene for Silver stealing the Pokemon could be really fitting. It would explain where Elm was when Silver was stealing the Pokemon.
But my personal opinion is that it is Elm's house.
Elm's house is moved atop his lab, making it perfect for him.
In place of his older house, a newer house will be there which is now going to be the home of your supporting character, just like Dawn/Lucas in D/P/Pt.
XD, I wish what you said was true.
What if it really is? :D