could be done but you'd have to write a bootloader that could read from the EEPROM. Not impossible, but not for the faint of heart. There may be one available though!
I can't really use an atmega328 because of all the components the project will require...
I planned using an Arduino mega and making a cartridge with an atmega2560 would not be so practical in terms of pricing if I want to make lots of games.
May it'll be that hard making a custom bootloader?
Another idea I thought of was putting .hex files on an sd card and loading it using a data logger shield...
It may be useful for. me but if I plan to sell the thing people are gonna make other copies of all the programs...
An EEPROM chip can still be duplicated but less of those are gonna be on the market than .hex files and thus, protecting me from losing too much money in that project.