Uncharted and Tomb Raider. It would make for the best co-op, action adventure extravaganza...plus i kinda wanna see them get it on.

Sonic x Mario? idk I guess I'll use it to get into sonic games

Jazz Jackrabbit X Sonic The Hedgehog. *Psyched*

Nope. 

A smash Bros like game only with Microsoft franchises and add Naruto Uzamaki and Ichigo Kurosaki in it.

Zelda x Final Fantasy or Zelda x Dragon Quest.

Monster Hunter x Pokemon?

Guess that might scar kids with you going around killing Pikachus...

The World Ends WIth You and Shin Megami Tensei

Concept:

Both series are in the broad JRPG family and feature the real life city of Tokyo in a contemporary setting. Even zooming in on Shibuya, many Megaten games feature this neighborhood, including the recent SMT4. Both TWEWY and SMT also confirm the existence of multiple universes within their canons. The head honchos in TWEWY, the Composer and Producer, are essentially deities tasked with mantaining and supervising the supernatural happenings in this area, similar to many Megaten demons, and have shown the ability to travel between alternate realities.

It is therefore pretty easy to make a connection here. The predominant antagonist in the Shin Megami Tensei series is YHVH, who is basically the physical embodiment of Tyranny, regardless of what some characters say. The series also implies that he is part of an entity that can be continuously reborn, and is responsible for the destruction of thousands of inhabited worlds that he was not satisfied with. So imagine the alarm of the Composer and Producer in TWEWY if he sticks his nose in their neighborhood. They would get Neku, the main character, involved if necessary.

Meanwhile, the SMT universe is already rich with characters who have resisted the forces of both Lawful Evil and Chaotic Evil. Let's go with Flynn, the protagonist of SMT4. Assuming that you get the hardest ending (aka not nightmare-like), he will have protected his version of the Tokyo region against a number of major enemies while ensuring it a powerful guardian deity.

My idea is that in order to stop YHVH and company from going on his rampage as usual, the benevolent entities in the two continuities team up, and connect the two games' protagonists so that they can fight off powerful evil entities in both worlds. At once.

Actual Game

This would be a 3DS game, just because. Take the basic combat of The World Ends With You, place Neku permanently on the bottom screen, and FLynn on the top screen. Neku is controlled via touchscreen while Flynn is given combos to execute using buttons on one side of the 3DS. Both characters can be heavily customized by collecting abilities from defeated enemies.

The "World" is just Tokyo, maybe not even the entire city. However, the gimmick is that this game takes place in two versions of it at once. Sort of like the Link to the Past Light/Dark Worlds, but each protagonist remains in their own version much of the time. Therefore, the game's exploration is heavily based around finding the many connections between the two planes in a relatively small area, rather than finding new horizons.

Various elements from the two series can be picked based on the story and world design. The Pin and Demon systems can be conflated, the metaphysical properties of fashionable clothing can be combined with that of technicolor armor, and stuff like that. Leveling up could be just one way of strengthening a character, along with the equipment, a good diet, demon fusion, etc. More variables is a good thing in this case.

The two protagonists will be in constant contact. It could be telepathy or whatever, but their dynamic needs to be constant. The theme of TWEWY is a more mature version of "Friendship is Magic" that Kingdom Hearts has been repeating for years, and SMT4 emphasized that humans have the ability to change their world for the better. These two themes can be exchanged between settings and form a cohesive narrative, where the two heroes' journeys prove the themes of both series.

Last, the Final Boss has to be against YHVH and Satan AT ONCE, on the two screens. Partially because it shows the power of the human duality over the divine duality, and partially because that would be one of the most awesome boss fights ever.

Wow, such a well thought out game idea! These two games does seem to fit very well together.

Zelda X Monster hunter
A zelda game with exploration and puzzles but with overworld action, combat, and RPG elements more similiar to monster hunter. you can through some skyrim in there for good measure too. and why leave Fable out of the Party?

Rhythm Heaven X Paper Mario
Take the action command based combat of the classic paper mario games and combine it with the rhythm heaven gmeplay to form a new genre- the Rhythm RPG!

Nintendo Vs. Campcom
this has already been said too many times but its really a good idea...

Boom Blox X Minecraft