That literally makes no sense whatsoever. Absolutely none. Take a look at the download sizes for MGS 2 and 3, separately, for the Vita. Even if taken separately, that's a pretty big digital download, right? Now decompress them so they aren't made necessarily smaller for downloading (ALL digital content is compressed, or it would be even more space on a memory card, much less a cartridge), and realize at the same time that flash memory costs the exact same amount regardless of the wildly variable cart size. The only reason it costs *us* more is because it would be stupid to sell the same size flash card at the same price, not because it costs a penny more to manufacture. There would never be a need for two separate carts for each game.
I don't get it. Maybe they want to start heavily pushing digital downloads even more, and they want the Vita versions of both X and X-2 out on the same day in case people want them separately, in which case it might make sense.