Having played both, I can tell you that Rugged Adventures is much more of a traditional minis game, but my preference is for .45 Adventures. I have to admit that I am not an unbiased observer, since I'm writing a new game based on .45 Adventures*. Both games have an excellent pulp feel (with a decided edge going to .45 Adventures, I think). There's a battle report here on an adapted .45 Adventures game used for a Cthulhu game, so you can see it works pretty well. Neither system has anything built into it for the lovecraftian genre.
Both games do better with a GM to control random events, and in .45 Adventures random events and encounter markers are crucial to the success of the game.
*The game I'm writing is a swashbuckling version, called Gloire.