for example we can increase the size of armoury to add room for more items, increase the size of team from 15 to 20 units if we want and they all will fit screen
Scrollbars.
Scrollbars are a bad idea, they make interfase much harder to use (you don't see all the available options at once). If we can place everything on the screen (or several screens), that is IMHO a much better solution. Also scrollbars need some time to implement and make code somewhat more complicated and harder to maintain.
Chat console font will look much better using higher screen resolution
I't looks good enough on 640x480.
It does not look good for me. When making it larger (SHIFT-'+' key), currently used
DejaVu font becomes much more readable. Looks like pixel size 12 is optimal, in 800x600 screen resolution is has almost the same size on screen as current 9 pixels size in 640x480, but has much better quality. And about the idea of replacing font with a better one, do you have any suggestions (it should be free and support unicode)?
And everything would be too small and the whole atmosphere would be gone.
I don't think that the whole atmosphere depends on the units size. Quire the contrary - you will see a larger part of battlescape on a single screen, that is easier to track what happens around. By the way, starcraft2 units are even smaller, but nobody complains. What are you trying to see in the unit sprites, missing some familiar big square pixels?

Indeed, you could use something like the scale2x library:
http://scale2x.sourceforge.net/
Thanks, I already know about this library (and also about hq2x, 2xSai and the others). The problem is that as any other feature it needs some time for implementing. And as I do not see it as a useful feature for myself, it is in the bottom of my priority list. But maybe you can convince me that this is really useful

Or even better, somebody could contribute a patch

Currently more people have voted for increasing screen resolution. But maybe we can postpone that until 2x scaling for battlescape window gets supported. Any objections to this idea? One potential problem is that the game will become slower in this 2x scaling mode, but we need to try it first.