Here's why: On an ARM-based system native apps are almost always going to be superior to browser based versions for one specific reason, efficiency. ARM is not a "general purpose CPU" like an x86 chip is. It's designed to run a subset of code very efficiently (remember, ARM is essentially a RISC-based processor architecture). You can optimize for it, which will help with performance and battery life. IE11 is great because it's a full-fledged browser, but that doesn't make it the answer for the missing apps. You also have browsers on all other platforms, but that was never a valid reason to not want the apps. I want native apps on the Surface 2 for the reasons I stated. I can do without them because of IE11 (just like I could on any other platform), but I still want native apps.
Here's a perfect example. YouTube on WP8. A native app is a much better experience (in more ways than one) than the m.youtube.com that's the current "official solution" right?