Hi,
This is my first post on here, so I'll just say what a great game this is shaping up to be before I say anything else...
Anyway, UFO Design.
The way I see it, there're a few things to consider:
As you've pretty much said, you need to bring out the bigger guns (and UFOs) as the game goes on to have a sense of progress. It's easy enough to explain in the story-line too.
I think the biggest question is, are they going to run on fuel or get power by some other means? The main difference it'll make is later in the game, if you're having to get the fuel either by shooting down UFOs or in some other way.
I reckon it'd be best needing fuel, having to shoot down UFOs to collect it and later on learning to make/refine your own.
Thinking about it, you're not likely to find the fuel stored in the engine, but in a separate storage area, a fuel-tank if you will...
If the fuel's normally stable it's unlikely to be destroyed in the crash, and if it's unstable it'll be stored in special tanks to prevent it exploding.
As the maps have to be pre-rendered, how are crashed UFOs going to be handled? Presumably it's not going to be possible to have random damage to the UFOs? I think if this is the case then I'd rather have some plausible reason why the UFO is (visibly, if not actually) completely undamaged after the crash, instead of the same damage every time.
I had a couple more thoughts but they'll do for now.
Tom