As for buying ships, it really depends on your goal. The game gives you a free ship at levels 10, 20, 30 and 40. The equivalent store ships are only marginally better than these free ships. So in my opinion, there's not much gameplay value in buying store ships until you're level 50.
Also, never buy odd-numbered weapons/consoles, and rarely buy even-numbered ones unless you're just stuck in a level and need an edge.