I honestly don't see them releasing both versions (handheld and console) of a game in the same cartridge. I fully understand there are benefits by doing so but at least I can think of one or two odds by pursuing such goal and most of them come from the handheld division.
1. With the current pricing model, either the console or handheld will have to give in.
Some time ago someone mentioned about a flexible pricing as: X game can be $40, Y game can be $50 and Z game can be $60 depending on the work done and IP.
Say Mario Kart 9 is one of the $60 games, it would negatively impact their business from people who have been playing exclusively on handhelds and refuse to pay $20 more for the assets of a game (console version) they will not play at all.
2. Packaging both versions in the same cartridge would mean they share the same box and retail space. Even if said box has neon lights shining bright saying X game is strictly console exclusive (because there definitely will be) there's a really really high chance people (parents mostly) will ignore that and still purchase the game for little Timmy's handheld, leading to a lot of problems between parents, retail stores and Nintendo itself.
The same will happen for handheld exclusive games.
Well, ask the cashier if a game works for X device first before buying!!! - Some of them are even clueless than the costumer, don't care or simply will say anything in order to sell games.
3. By releasing both versions in the same cartridge Nintendo basically would cut a big chunk (over half) of their revenue from those who actually bother to purchase both of their platforms and wouldn't do it anymore because the game is basically the same between devices**. Nintendo first and foremost is a business so I don't think it's the smartest thing to do.
Now, I know they already have quite a few titles that allow cross buy where you purchase one version and get the other one for free but that's mostly for smaller projects. We have yet to see it working grand-scale with all their AAA IPs.
**This is more of a side effect of unifying their development teams as those who usually get both platforms get them because of the different experiences each game has to offer compared to the handheld/console counterpart.
. e.g. 3DS Super Mario 3D Land -- Wii U Super Mario 3D World.
Now it would simply be let's say... Super Mario 3D Universe for both platforms.
This is basically when exclusive games for X device come out to play.
IMO they'd be better off releasing disc versions of games for the console and cartridges for the handheld. It really boils down to how clear their message is, how the games work and how their marketing handles the promo.
For some reason, some people have come to the conclusion that merging their development teams instantly means cross-buy//pay one get two kind of deal when in reality (and what we know so far) is merely to make it easier for them to create and manage new projects across devices after struggling to support both with a healthy and steady amount of games for years.
They way I see it, Nintendo will offer the same game for both platforms but ultimately it will be the costumer who decides what versions makes the most sense for him/her.
Now, I think however, they won't have any problem offering a digital version for free when you purchase the other one and/or offer X digital version at a heavily discounted price when you purchase the other one for some of their games (if not all of them). After all, that's the whole point of "brother/family of devices" or the infamous "shared library" concept but from that to offer both versions in the same physical medium is quite a stretch imo.
EDIT: In case it comes the wrong way, I'm not opposed to the console using cartridges AT ALL, if they can do it then that's great. My post is more towards sharing a single game/cartridge between both platforms.
