The problem is cost of entry into the market with diminishing returns.
What we have is not a technology problem. The problem is that what you build is worthless unless you get people to adopt it. And right now, that requires:
* Building a phone/piece of hardware that can run apps and replace the iPhone/android phones
* Investing in a marketing campaign to get your hardware into the mainstream, so people will buy your phone instead of an android or iphone.
* Convincing companies and app makes to build for your new hardware.
That breaks down to a tremendous amount of R&D, building a cloud network that can rival Google's and Apple's cloud systems, convincing app makers to build for a platform despite it not having any users, and convincing users to buy into your platform despite not having any apps.
It's tremendously expensive.
It was a worthwhile expense for Apple: they literally invented the new ecosystem and were the only option at the start. Their return was guaranteed.
It was a worthwhile expense for Google: they already had the cloud services, were a household name, operated arguably the largest ad network to market their new platform, and had plenty of cash on hand to get things moving fast. They may not have been able to match Apple's competition-less returns, but had a low cost to entry and even half of the pie is great value.
For any new competitor, having to share the pie with Apple and Google limits the potential return. Couple that limit with having huge expenses to build out a competing product and getting people to use it, and it's not a very appealing investment. At best, you get what's left after Google's and Apple's shares. At worst, you spend millions (billions?) for nothing. We've already seen the Windows Phone and the Fire Phone fail to enter, and if giants like Microsoft and Amazon deemed it not worth their while, who will?
So that's where we are now. So long as the masses use Apple and Google products, they will continue to default to those app stores. And it doesn't make financial sense for anyone to enter the market and compete with them (with any significance, at least).
I could see some very niche phones/tools coming into play, but with very limited functionality and only a narrow user base that actively seeks that niche. Eg. security-seeking engineers. Someone could make a phone with very limited features (at least, "native" functionality ala gmail) and see success with an audience seeking that subset, but it wouldn't be a mainstream option.