I would like to point you towards
SFS, which was designed by a certain one of the mods here (who apparently declined to engage in blatant self-promotion in his earlier post, a tactful move I can appreciate even if it doesn't really help the conversation). It is not significantly more difficult to support than FAT - in someways it is simpler, really - but is completely unencumbered to the best of anyone's knowledge (though that might not stop some patent trolls if they decide it violates some IP they bought that was patented at some point, even if
the patent has expired, was never actually accepted, or was submitted after SFS was published - all things we've seen patent trolls actually do in real cases).
However, regarding flash drives and memory cards, you will note that Microsoft aren't likely to file a suit against you unless and until your OS becomes widely used - it simply doesn't gain them anything, even in terms of the requirement that they defend their IP in order to retain the patent. This is definitely a case of it being easier to ask forgiveness than permission - go ahead with the implementation, and if they throw a Cease and Desist order at you, you can drop support for it before it goes to court.
This is one of the things that differentiates a corporation like MS, Apple, IBM, or Oracle, and a patent troll. While the bigger players can be total Richards about their IP, this is mostly because of the requirement that they consistently defend their IP without favor - the rules state that if you don't defend the patent, trademark, copyright, etc., or only defend it against certain parties and can be shown to have deliberately ignored infringement by other parties, then it becomes invalid. They are usually more than happy to make a license agreement (if you can pay and are willing to abide by the terms - which are the two places where they are most likely to stick it to people), and as a rule won't pursue someone who has stopped actively infringing and has removed existing violations from use. Most corporations will open with a C&D in a neutral tone, then step up the threats by degrees,but if they are unable to get what they want from you, they
will hit you in court, hard.
Patent trolls, on the other hand, tend to start with a demand for money backed by a threat of massive legal action, and will keep asking for it even if the 'infringement' has stopped, even if the IP is shown to be invalid or expired, and even if they have actually been defeated in court on the topic by someone else already - but will often back down the moment you show a willingness to fight.
The 2013
Prenda Law case is pretty typical of this sort of shakedown, if rather more blatant in its disregard for the actual legality of what they were doing. I also direct your attention to the recent
Wetro Lan case - while they stuck their willy in a meat grinder that time, they had been doing this sort of thing for quite a while beforehand and this was their first real setback.
My point is that in terms of IP, the big boys aren't the ones you really need to worry about, at least not until you are big enough to get on their radar. The ones to be concerned about right now are the ones who are in it purely as a racket.
$$ for M$.