As was mentioned adapting one game into another with your own themes and whatnot, something that may fall under the banner of total conversion, is one of the more intensive things you can be doing as a ROM hacker.
Likewise ROM hackers tend to be made up of those that will push through a challenge, and probably even enjoy doing so at some level -- I won't be happy to spend all weekend essentially piecing random data together but if at the end of something when it all clicks and I finish up with "well that was a need trick and an interesting way of doing things" then I like that and I dare say I am not alone in that one. There might be ROMS out there which are basically ASCII text with raw memory locations preceding it (and in text markers to match), graphics that are uncompressed and unmapped 8x8 or 16x16 tiles, fonts similarly basic and with plenty of space, levels you can practically paint in a hex editor if you set it to the right width, stats you can read no harder than looking at a spreadsheet, and so on and so on. I don't know of any offhand really and ultimately such a thing would teach you nothing, or at least not prepare you for the real world as it were.
If you want to practice individual skills there should be enough documented ROMs out there that you can fill in the gaps, or not have to worry about doing the boring initial steps to get to the thing you want to learn. Again I don't know of any one ROM that has it all but there should be enough simplistic examples out there to switch out as necessary.
For instance if you find an existing encoding table for a game you can drop parts and fill in the blanks and practice finding punctuation. If you know where text is because something told you you can find out a table even if you know nothing of the encoding. If you have a full table and text you can then work on pointers. With all of that you can figure out how to make a script for the likes of atlas and cartographer or one of the other text dumping/insertion setups. If you know where graphics are located for a game you can instead learn your tile editor more easily and possibly then figure out palettes and workarounds for them. If you have a level format dictated to you then you can either fill in some blanks or edit it raw and learn how such things work (nobody will practically edit a level raw but if you understand what is going on underneath it all then so much the better). This goes on for a while but there are plenty of ways you can have the grunt work done to the point that all you have to do is what you want to learn.
I don't know if there is any one system I would suggest. When learning assembly or something you might get the learning CPUs that don't do anything exotic, and in electronics for consoles or emulation you find yourself staring at the chip-8 stuff. Practical realities of electronics, economics and people being more than happy to trade increased complexity for increased capabilities mean there is not a lot here.
Different ones have different perks -- while the GBA and DS might have their quirks they are ultimately fairly textbook examples of all the aspects of game consoles and something you will never run out of space for. They might have more complexity than the NES but it is still fairly obvious expansions of concepts you will find there.
You probably want to pick something reasonably popular (most Nintendo consoles/handhelds or 8 or 16 bit Sega efforts or the game game, PS1 and PS2) and there are some I would not pick (probably arcade and Sega Saturn, might include N64 in this too) for complexity reasons, and go too new and you end up basically doing a slightly more exotic version of PC game.