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Considering the significantly better rendering capabilities of the 3ds when compared to the DS, I'd say you won't see a ton of FMVs to begin with. You can fit a lot of stuff into 2 Gigabytes worth of cartridge space when you don't have to store 8 or more texture passes at high resolutions for every surface. Burnout Paradise, which is a gorgeous racer and even open-word, takes up less than 3 Gigabytes iirc. Also, since cartridges have significantly shorter access times and faster reading speeds then say, the PSP's notoriously slow UMD drive, there isn't a lot of need to cover up loading times with FMVs either and you can use much more aggressive compression technologies too. Resident Evil 2, which was released on 2 CDs originally, fit onto a single 512 Megabit N64 cartridge (that's like 64 Megabytes) Regarding flash memory: it's certainly not that expensive anymore and is going to get cheaper and cheaper as time progresses, but it's also very, very slow, especially at large sizes.
"If god didn't want us to eat in church, he would have made gluttony a sin." - Homer Simpson