If you get a Surface Pro, that is nothing to worry about. There are WAAAAY more apps for Windows than there are for Apple or Android. And a Surface Pro will run them all, just like a regular desktop PC running Windows 8 Pro. The MS App Store thing is only a concern if you're buying a tablet that's running Windows 8 RT (e.g. a Surface not-Pro).
Not quite... Windows apps were developed to be used with a mouse, not a touch screen. Also, most Windows apps are resource hogs. Windows, itself, is heavy and a resource hog, all meaning it requires hardware that drives cost up and the consumer out of the market. Android and iOS apps are specifically designed to use with ARM type processors and are lightweight and task specific on purpose. Also, the app prices are spot on in Android and iOS. Full Windows software applications are plain expensive, but worth it if you need that level of power, which most tablet users won't.
There was a Macbook available as a tablet, called the Modbook, long before the introduction of the iPad. It didn't sell well, either. Tablets are nothing new, but when the iPad was released with inexpensive apps, speedy ARM processor, long battery life, an entire ecosystem around it, and a relatively inexpensive price, it changed the game. A full Windows 8 Pro tablet won't do anything.
Lastly, whether or not it's for the Surface RT or Pro or the desktop version, I believe that Microsoft requires the use of their app store by anyone using the Metro UI for their applications. If you use the classic UI, then you're free to do what you want.
Microsoft is lost in the new landscape. Windows Phone 7 failed. They, then, force the Metro UI on the rest of us with Windows 8. It's failing as I write this with sales slim and flat. Surface has bombed. What next for Microsoft? They're quickly becoming a niche player that has run out of ideas that actually work. They can no longer bully users and OEMs around because their products are yesterday's news.