Man, that's a TOUGH choice. I'd say get both, but that's the easy way out, right? I guess it depends what type of gamer you are or what your tastes in games is. Personally, I'ma big fan of the FPS genre, so BF 1943 was a no-brainer for me. I've already put 30 hours into it, so it was a 15 dollars well spent. Although there are only 4 maps for the game, the openness provides all the variety you need. I love it.
On the other hand, from what I hear, Shadow Complex is an amazing game and a steal at $15. I will get this one eventually as well, but not having played it, I can't offer you any insight on its quality. It was strongly inspired by Metroid, and that's all I really need to pick it up.
Bottom line: If you're a multiplayer, FPS fan get BF 1943. If you're not really into multiplayer games and are content to go solo, SC is the game for you.
Oh, and what't the anti-gay controversy surrounding Shadow Complex? This is the first I've heard of it. Compared to most of the idiots on Xbox Live, it must be bad to be considered anti-gay....