When a product is covered by more than one patent, the patent-holders end up in a tragedy of the commons problem. The commons is the person with the product. He has money he can pay. Each patent holder has a veto over the product and wants to extract as much as they can. One hold-out can ruin it for everyone and every single stake holder often ends up worse off as a result.
The cases you are referring to - where there are blocking patents - generally are resolved with mutual licensing agreements. Of course, there are many exceptions, especially when there are patent trolls involved.
In these cases, though, I really wonder the comparative cost of innovation versus licensing battles. Software is still an amazingly open field - given that licensing battles can run into the millions, if that money was invested in R&D could an alternative (superior) method be found?
One of the methods that patents were supposed to encourage innovation was by providing reasons to innovate. If you are forced to explore new options and develop your own IP that might be patentable, is that such an awful thing?
Software patents often leave zero room for innovation. Let's say you patent pushing email to a hand held device AND pulling email from a hand held device what are the options? Showing a screen shot of another device that's not hand held? It's still either push or pull. etc.
