Any ideas?
Concerning the crystals part, how about this:
The eastern base contains no (significant amount of) crystals, but it's
a factory. It doesn't have the hovercraft, but the player starts out
with a personnel carrier. When the player conquers the base, put some
crystals into the starting base (in case he used those he had from the
beginning for repairs). The player needs to ferry enough crystals from
start to factory to build a hovercraft which he can then use as you
described. That way you won't even miss the "amount of crystals in a
base" trigger (which might be useful nevertheless).