The side missions are indeed pretty samey, but I couldn't imagine not doing them. Repetitive? Yeah a little, but I've yet to play an RPG that isn't.
Besides, driving the MAKO is fun, even if it made me feel like the universe's worst driver.
What threw me about the side missions are how hard some of them are early on. Because so many are available to you almost right away, I expected them to be fairly manageable at my current (at the time) strength. But after having my butt handed to me a bunch of times, I realized that was going nowhere fast. So I went back later and romped.