I don't think what you have in mind is really possible. You have to realise that you are playing old games, and the pixelated graphics are what we really seen at the time we played those games.
I know it turn off several people, but the gameplay is there and is excellent. I would rather play Xcom again than Aftermath anyday. Same for the old classics like MOO, Civilization, etc.
Just don't forget to hit alt-enter before playing so you are in full screen. Maybe that's why you see the graphics so small.
If you have any other questions, feel free to ask away here.