It appears to me that:
1. B&N is arguing that Microsoft's patents are invalid based on prior art rather than that Android does not use the methods covered by the patents. This makes Microsoft's assertion of their interest legitimate even if their patents should be overturned based on prior art (or if software patents themselves ought to be abolished, altogether). This form of competing claims is exactly the sort of matter appropriate for patent litigation.
2. Given their financial situation and the choice of the Nook's operating system being non-central to B&N's overall profitablity, it seems to me that B&N's decision to litigate (somewhat on Google's behalf) seems to be an attempt to swing for the fences and hope for a big settlement rather than focus on business fundamentals.
3. The DOJ appeal seems particularly week given the market share of iOS devices.
This seems like Microsoft is still trying to stay relevant via patent litigation rather than actual innovation. If WP7 tanks, then they are still getting the same amount of licensing fees for every Android handset sold, so who cares (from their perspective) that WP7 tanked...
[IANAL]
To me, equivalent pricing seems to be plausibly consistent with the fair market price of a mobile operating system which incorporates Microsoft technology... [edit] at least from the perspective of a lawyer representing Microsoft.[/edit]
It is hard to argue that Microsoft is placing Android at a disadvantage relative to WP7 when the price is equal since this allows Android to compete upon its technical merits and any perceived market advantage the brand provides.
2. The choice of the Nook OS does affect their profitability, cost control is the primary way a company can gain price flexibility / increase margins. Using Android means no license fees, no restrictions on how you implement it (apart from those you impose on yourself and / or technical limitations). B&N will probably have a large sunk cost on research, development, and operations by going with Android; doubling or more of that sunk cost because of a "bully" will put the back up on more than one or two execs. B&N are probably feeling they are at the point that it might be cheaper to litigate, or they feel that this might be a bet the company moment.
3. If you are going to take a punt on some anti-trust action you don't instruct teams like Cravath; you go to them if you feel you have a good chance to prevail or have more money than sense; B&N at first blush don't strike me as the second.
[IANAL]
If Microsoft's patents are not infringed or they are invalid, that is correct.
However, the former does not appear to be part of B&N's argument, while the latter is obviously subject to debate at this time.
Therefore, it appears to be premature to assume that this premise of your argument is well supported from a legal standpoint.
The only reason I am not buying a couple more is that they are only supposed to be used in the US, unlike the Kindles.
edit: I forgot the "burn, karma, burn" line.