I'd treat megascale and normal scale as different realms, metaphorically; for game purposes, some things happen in megascale, others happen in normal scale. When you're travelling cross-country you're operating in the megascale realm; when you're in a fight you're operating in the normal realm. If you buy just one, your power only operates in that realm; if you want both, you need to buy both, usually in a multipower.
If you just buy megascale movement you're saying "My movement power is good for travelling huge distances quickly, but not useful in fights." The specifics why it's not useful could be thought of as inaccuracy, turning limits, extra time, whatever. The exact reason really doesn't matter; for game purposes it just means your power can get you to the fight quickly, but has limits such that you don't use that power during fights.
Whereas if you buy both megascale and normal versions, in a multipower, you're saying "This is how useful my power is for travelling huge distances, and that is how useful it is for maneuvering around a battlefield." Comic-book characters would have that multipower if their powers are useful in both situations. And you'd simulate their specifics by varying how much normal scale and megascale they have; some characters are better at the tactical than the long-distance, while others are the reverse.
It's a game construct, but it strikes me as a useful one. You have your tactical battles, and you have your long-distance trips and plot-device weapons and so on, and they're pretty much separate aspects of adventures. So it makes sense to define how good a character is at each separately as well, rather than to start with a single power and try to flaw it enough so the megascale capabilites don't turn into overwhelming tactical capabilities.