Well, I own both games and they both have their charms...
Runewars is a bit easier to learn and play, making it a better choice when playing wih people that are not regular players of FFG big box games. Another pro for me is that it's based in the Runebound/Descent universe, making it quite easy to grab if you know those games. A little contra in my opinion is the fighting system. The card based system is interesting, but uses a bit too much luck for my taste. A second one is the gameboard. sometimes there is not enough space on the tiles and they tend to move on the table too much.
Starcraft on the other hand brings in the complexity. The order system makes a great starting point for a wide variety of decisions, giving you more flexibility. The fighting system is a bit better than the one in Runewars, although I also don't like this one too much. Additionally I like the miniatures from Starcraft much more than those of Runewars. Unfortunately they are also a contra... The plastic stands of the flying units tend to break. I also think that the units are all much too close together regarding strength/combat effectivness. But that might just be because the combat system itself doesn't favor my style of playing.
Compared I have to admit that I can't give you a singular advice. I like Starcraft more, but that's mainly because I prefer SciFi to fantasy. ;-)
Greetings from Hell