Cost is definitely a huge thing, if not the biggest thing when it comes to the actual product and production. I am a jack-of-all-trades who needs a lot of graphics for this project, so something like the MMC3 is ideal, and I don't have to pay an artist because I'll be doing it myself. But discrete parts are super cheap (like 20 cents per chip) and if all you need is 8 kb of CHR ROM or something then using MMC3 "just because" is just throwing your money away. Not only that, but when I was working with the UNROM format, I learned a lot while trying to tackle the various issues I was having with its limits, which of course is invaluable.
The main reason I am developing a new game for the NES is BECAUSE of the limitations. I find they force me to think in ways that I otherwise would never have given the virtually unlimited freedom of, say, PC development or Flash/Air. The constraints are what drive me to push the limits of the console as well as my own limits of creativity and problem solving.
Either way, at the end of the day, Super Mario Bros is NROM. Enough said.
