I don't think Microtransactions make a game bad, but I avoid games with them as a matter of principal. DLC is fine so long as it isn't cut from the original game. I mean imagine if the Forest and Shadow temples were cut from Ocarina, and then added on for $10 a pop. Or imagine if the challenge stages were cut from Mario x Rabbids and sold to us as a $10 DLC pack. 

Games are difficult to make, and sometimes content is cut just because its not ready. You cannot get mad because a 40 hour game has had a 2hour content cut from it and then sold as DLC. Basically you have to take into account if the game is worth the cost when it ships.. not some arbitary well they were making a 100 hour game and feeling like you've been robbed. The cost to make an AC game, most of the time you cannot feel robbed. Now I do agree when they cut out chapter 13 from AC revelations I think it was, I wasnt too happy as that was core story content. But if its a set of side missions, nah not a problem. 

So in your example, if challenge stages were cut from mario, well is the game worth the price of entry without those items. If you are talking modes I might agree in some instances (like I wouldnt expect to pay for a last man standing mode in Multiplayer games) but if its story content that is extra missions, I am ok with that, especially with AC games where there are lots of story based content already.