They actually did answer "why not just clone the science guy" in the movie. They already had a person to run the avatar, the guy's twin who happens to be an ex-Marine. They established that the corporation doesn't really care about the science side, so having a jarhead run the blue puppet makes perfect sense to the bean counters. Why spend money to clone and re-train a "science puke" when you already have a viable replacement, someone who could be just as useful just in a different way? Basic corporate logic.
Now... As for cloning the bad guy... WTF? Why would they do that? Aren't there any other ex-military mad dogs back home that could step up? Going back to the corporate logic, why clone when you can just find another to step in? That seems like excess expense for a company that's supposedly in deep fiscal sh*t.
(and... dang it, MartyS hits my points just before I can post them...)