Two years into the creation of the Windows Store, Microsoft is facing up to the mess.

This week, the software giant removed 1,500 "misleading apps" from the Windows Store. New apps now face tighter guidelines, and Microsoft says it's putting more resources into identifying apps that "game the system with misleading titles and descriptions." In other words, Microsoft is trying to clean up the lame shovelware and outright scams that run rampant in its app store.

The crackdown may have been a response to recent reports that pointed out just how bad the situation has become. But there's a larger reason Microsoft needs to whip the Windows Store into shape right now: The Windows Store will be making a major push onto the desktop in Windows 9, and it needs to be presentable or else those desktop users will be turned off for good.

The bland reality of desktop software

Only the most grizzled Windows veteran would contend there's nothing wrong with the status quo. For too long, the Windows desktop has lacked a centralized—not exclusive, mind you—app store, and the Windows ecosystem is suffering for it.

A centralized store is more than just a single place to find, purchase, update, and manage all your software. It's also a place to set standards, so that programs share common features and have a unified look and feel. The Windows Store, for instance, introduced a modern design language, enforced support for high pixel density displays, and gave apps a powerful way to share information amongst themselves. It also introduced "Snap," a feature that allows apps to remain useful even at reduced window sizes. If recent rumors are correct, future Windows apps could provide rich notifications and tap into Microsoft's Cortana virtual assistant software.

Windows Store apps play nice with high-resolution displays and automatically adjust their interface when "Snapped" alongside other windows for multitasking.

Without these things, Windows software is stuck in the past. Too many desktop programs look like they were designed at the turn of the century and don't support modern technology advancements such as ultra-high resolution displays. You're never quite certain whether that random .exe file you just downloaded is safe, and you have no easy way to re-download all your software when you install a new machine. For all the talk of Windows' vibrant desktop ecosystem, most desktop users likely have a handful of old standbys—things like Office and Photoshop—and don't bother to venture much further, despite the wealth of superb lesser-known software that's out there. It's easier to stick with what you know or stay in the confines of a web browser.

The Windows Store could have been the answer, but it wasn't the solution that laptop and desktop users were looking for.

The Windows Store's big pivot

A couple years ago, the Windows Store's prospects seemed a lot brighter. Although Windows 8 had its detractors even before launch, Microsoft hoped people would warm to the new modern interface and adopt a new breed of full-screen, touch-optimized apps. In turn, the platform would flourish on PCs and mobile devices alike, as developers lined up to support an operating system already used by hundreds of millions of people.

Instead, Microsoft received backlash, as most people continued buying traditional laptops and just wanted their old desktop interface back. Since the launch of Windows 8, Start menu replacements like Classic Shell have notched millions of downloads, and Lenovo—the world's largest PC maker—started pre-loading its laptops with a Start menu from Pokki. Speaking to PCWorld last year, Asus chairman Jonney Shih said that "the hottest app, sarcastically, is the one that puts the Start [button] back."

Soluto People just don't use Metro apps very frequently, according to a 2013 study from Soluto.

As the masses fled from Microsoft's new interface, they left the Windows Store behind. A May 2013 study by Soluto found that people barely touch Metro apps. Nearly two-thirds of laptop and desktop PC users launched less than one Windows Store app per day. Even tablet and touchscreen laptop users were launching less than three apps per day on average.

Without many people visiting the Windows Store, developers didn't have much incentive to make apps for the platform—and to adopt the necessary programming tools to do so—which in turn dissuaded people from visiting the store. The vicious cycle was in full effect.

So last April, Microsoft revealed its Plan B: A future version of Windows will include a reborn Start menu for launching classic and modern Windows Store apps alike. Those modern apps will then be able to run in windowed mode on the desktop, where they can be managed from the taskbar. For desktop users, running Windows Store apps will no longer require a change in workflow. And the Windows Store itself already comes pre-pinned to the Windows 8.1 taskbar. If Microsoft can just convince its huge base of laptop and desktop users to visit the Windows Store, those app developers might finally follow.

Windows 9's app-compatible Start menu and ability to run Metro apps in desktop windows is Microsoft's chance to integrate Windows Store apps into desktop users' workflow.

This plan falls apart, however, if Microsoft's store is filled with junk.

Having it both ways

A recent report by How-To Geek—probably the one that prompted Microsoft's sudden attention—details how bad things had become. The site pointed out dozens of fake, paid apps masquerading as popular programs such as iTunes, Firefox, and VLC Player. Often times, these apps were just paid "tutorials" teaching people how to download the real thing from outside the store. Although misleading apps aren't unique to the Windows Store, other app stores do a better job of hiding them or surfacing search results that are actually useful.

Clearly, Microsoft is doing the right thing by cracking down on these misleading apps. The question is how quickly and thoroughly Microsoft can clean things up, and how many apps it's willing to purge in the name of quality. That's where things get tricky.

It's widely expected that the next major version of Windows will be a grand convergence. Windows Phone and Windows RT will reportedly combine into a single version that spans smartphones and tablets, while a more professional-grade version of Windows will focus on desktop use. Meanwhile, the Windows Store will reportedly span all versions, making good on Microsoft's long-term plan to have one unified experience across all devices.

But this mentality is what got Microsoft into trouble with Windows 8, and it becomes an issue again as the Windows Store makes its big pivot.

Mark Hachman Now playing in the Windows Store: Attack of the unofficial YouTube clones.

Here's one example: Currently, the Windows Store is loaded with YouTube clones of varying quality, ostensibly to fill in for the lack of an official YouTube app. The demand for these apps is great enough that they sometimes appear in Microsoft's top charts and get high billing in the store's video section. But for laptop and desktop users, these apps are worthless. YouTube's website is a much better experience, and unlike some of the Windows Store clones, it's free. Should Microsoft remove these apps or leave them in place for phone and tablet users?

And what about the rip-off apps that Windows itself sometimes suggests you install when you do a system search for a program by name, but the official program has yet to find its way into the Windows Store?

On laptops and desktops quality needs to reign. Instead of being a sprawling marketplace with lots of dark corners, the store must be laser-focused on unique apps for productivity and creativity with features that can't be found in legacy software. Otherwise, getting them to visit the store at all will be a tough sell.

The challenge for Microsoft, then, is to serve both interests in the same store at the same time. Can it effectively filter, block, boot, and curate apps on the desktop side, and still cater to the needs of phone and tablet users? Microsoft needs to figure it out soon, as the Windows Store is running out chances to make a positive impression.