I would posit the reason phone manufacturers are paying royalties as opposed to cross licensing patents is because Microsoft doesn't have enough market share for HTC, LG, (Google?), etc. to make it worth while for manufacturers to trade their patents for.
In other words, phone manufacturers see $10 (a guess) per phone payed to Microsoft today is cheaper in the big picture than licensing WP7 instead of Android on those phones. In addition, it implies they value their own patents more than that amount and thus refuse to cross license their own patents to instead of paying the Microsoft royalty.
The logical conclusion is that phone manufacturers have looked in their crystal balls and bet strongly against Microsoft. They are betting that, in five years (a guess), Microsoft will be out of the phone software business and their patents will be irrelevant because they have either expired or been worked around.
The phone manufacturers are also remembering the iPhone vs. Windows Mobile / Windows Phone timeline and remembering how long they were getting buried by Apple because Microsoft was not able to sell them a credible alternative to the iPhone. Screw me once, shame on you. Screw me twice, shame on me.