Unfortunately I've yet to hear of a way to resolve this since the keyboard is a fixed height/width and the dialog box for most apps are also. I had the same issue on my Galaxy Nexus and it bothered me to no end. I've just accepted it at this point. There's a post over on stack overflow about it but I think the fix they recommend is a developer thing; android - Landscape keyboard obscures view - Stack Overflow
Have you tried using any of the other keyboard options; one handed, left handed, right handed, etc?