EEPROM is used to store miniscule amounts of data in GBA, DS, and 3DS games, stuff like number of lives, completed levels, ranking on time attacks and times, etc. Stuff that takes up literally just a few bytes (typically). Flash is used for games that save lots of data (kilobytes to megabytes), these would be through a game that saves to flash an ideal overflow exploit would be executed. If you actually looked into overflows and how they worked, you would also know that games that use EEPROM to save typically can cope with values that don't work well (such as too many lives, 135/120 stars, etc) and know how to deal with those errors. Flash-based saves that have many kinds of variables, strings, and conditions (or even bits of code, a la Super Mario Advance 4 for the Gameboy Advance) are more likely to run unsigned code since it has the capacity to store the actual code.
The other thing is that if you are to use, say, New Super Mario Bros. 2 (which uses EEPROM to save) you would have to load the modified save, and hope that when the game loads you overflow at the perfect point where the game continues to read the save. Such knowledge would require 3DS emulation, extensive memory viewing, or ROM disassembly (which would likely have to be done by hand). Flash eliminates part of the lucky-keep-on-reading loophole you are unlikely to exploit, but even then you are pushing your luck with an overflow. Seeing as you aren't established in the hacking scene, you are trolling with talk of Wii emulation, and you can't back up your claims at all (have you ever disassembled a game, or tried modifying source code for a game?).
I'd say you are full of shit and need to find a better way to spend your time.