Definetly get the moonroof as it's all positives with resale value and I use mine. If there is a performance deficiency with a sunroof you won't notice it on the Focus.
I recommend extra tint on the moonroof glass;it will really reduce incoming heat much better than with the factory tint. I have 15% on mine which was perfect.
'12 Focus Red Candy SE Sport 5 spd
'99 Toyota 4Runner Sport
'11 Subaru WRX STI Hatch