If you plan on plugging into an Arduino you must keep the connecters in the same location and have similar function. The board however can be bigger.
Consider if you want to plug it into one of the solderless boards for testing when you place the connections.
I recommend what ever you do, keep the connectors and pins on a 2.54mm grid. And when I make a board I:
- Never make a connection under an IC (if possible) If you find out you need to cut it for some reason you won't be able to.
- I bring all µP pins out, even if it is a short trace I could later scrape the solder mask off and solder a wire.
- If you don't have a space problem you should add capacitors on the analog inputs, and maybe a resistor divider. You can always leave parts out.
- An on board LED is good for testing.
That's all I can think of for now.