Depends who you talk to.

They're completely different types of games. Civilization is a turn-based game (although the multiplayer uses a semi real-time system to prevent waiting for turns), and the matches are more stretched out, often taking a few days to wrap up a match. Playing against the AI is also the main focus of the series. There's alot more focus on diplomacy, technology, truces, trading, and such rather than combat (although combat is the main method you'll use to dominate other civilizations), which is very luck and rock-paper-scissors based. It's kinda like really controlling a country and trying to keep it under control while expanding and ruling as much as the planet as possible.

Starcraft operates in real-time, and plays very fast. Matches take about 20 minutes on average, and multiplayer is the focus, although the single-player campaign is absolutely phenomenal in Starcraft 2. The gameplay here more like a strategic Deathmatch, and overwhelming the enemy, controlling the map, and expanding as quick as possible is the focus. Combat plays a huge part here.

They play very different, so it's hard to compare. It's really based on preference, everyone will have a different opinion. If I had to pick one of the two though, I'd say the Starcraft games, especially Starcraft 2.

For people that like competitive games, Starcraft is much better.