I intend to develop games for Microsoft's Windows Store, however, I'm confused between their platforms, so please clarify those questions:
I will try to answer your questions to the best of my ability:
1. XNA allows you to develop games for those platforms.
MonoGame allows you to create games for the standard platforms as well as iOS, Android, Apple Mac, Linux and Windows 8.
Since XNA games are written for the runtime, they can run on any platform that supports the XNA Framework with minimal or no modification.
Source: Wikipedia page on XNA
Not sure what you mean by that but Microsoft owns Xbox and Xbox360.
2. I am assuming you meant to ask "What is the best platform for 2d games?". It is entirely up to you. Because of the hardware limitation on Windows phones, 2D games are pretty popular on the store (Also because of the touch screen, easier controls). It all depends on what you want (to make it for) and your target audience.
3. See quote from Question 1. As for the windows/phone store, I am not sure because I have not used them.
Hope this helps you!
If I understand you right, then, no, there is generally no single Microsoft technology that will allow you to cover all described platforms.
For Xbox360 your option is Microsoft XNA, DirectX development only allowed for certified studio developers and can't be considered an option for most of small development teams.
For Windows Phone you can also use Microsoft XNA which will run both on Windows Phone 7.x and Windows Phone 8 devices.
For Windows Store you can't use XNA, you need to either use DirectX or HTML5 based games.
However, you can use MonoGame to develop games for all of that platforms. While it's arguably considered pretty buggy, for a simple 2D games it's a pretty safe choice. The advantage is that you can use almost any XNA related sources and examples to learn MonoGame (since it's actually independent copy of a XNA platfrom).
Try using game engines such as the :
Unity (http://unity3d.com) (Battlestar Galactica)
Unreal engine. (http://UDK.com) (Mass Effect, Tera)
CryEngine www.mycryengine.com/ (Far Cry)
.
Both are multi platform game engines which come with a complete compiler and an advanced toolset. With these you do not have to worry about writing scripts for a particular OS. If you make an app for Iphone, it will have a different touchscreen UI (user interface) from the same app distributed for a PC with a mouse controller.
When it comes to unity you also have access to a large library of complete game objects that are ready to be implemented in your game.
And remember one important thing - Don't write engines that are already written. Because unless you want to join some large company and help developing a game engine you will have no chance to create an UP-TO-DATE GAME ENGINE, most likely you will end up with something compared to quake engine. But you will learn a lot.
XNA may be a good choice, if you want 2D and want to dev for Windows Phone and Xbox360. However if you goal is the microsoft store for Windows, then it may not be the best. However if you want to use XNA, you could post it on Steam Greenlight or something simaler. Some games made with XNA have become pretty big so It is a capable engine. Terreria , Magika, and Bastion are supposedly xna.
If the windows store thing needs DirectX/HTML Then something Like unity3d May be a great option. Unity doesnt have to be 3D if you dont want it to be. Ive seen some neat plug-ins for 2D games, and you might not even need them I havent really looked into it. Orthello is probably worth a look. : https://www.assetstore.unity3d.com/#/content/1014
