Well some time ago I heard something about some ppl trying to make a "Wind Waker"-mod for a "Zelda Oot"-ROM by replacing graphics and changing certain other things such as effects
(it's strange, I know, you would assume people to do it the other way around :p )...

That is what the article definitely is not about.

It's not about ROMs, but about the consolegames themselves, thus the possible changes do not include completely switched graphics and such (except if you're willing to enter a looooooooooooooooooooooooooooooooooooooooooooooooooooooooooo[...]ooooooong code just to change some textures), but instead the idea is to create new "rules" for the game so it gets a different gameplay... - by using IF-THEN-codecombinations...

(The most common example is a moonjump... Condition: IF you press L (or whatever other button it is in your case) THEN jump to enternity.)

How about a co-operative race in Mario Kart64? The only disturbance is that if player 1 gets a "flash", he'll have to either risk hurting his teammate or wait until his partner has found a proper protective item (which can take a long, looong time).
Sooo, let's change the rules a bit... IF "player 1 gets the item flash", THEN set "the item that player 2 will get by driving through the next itembox" to "a ghost" (which is an appropriate protection).
Therefore, the co-op gameplay is a bit more smoothe... and then you can think about the next adjustment.