The current arrangements represent a fairly good balance between cost, complexity, and specification. Thats not my opinion, its the opinion of almost everyone in the business. There are over 20 steps in the supply chain for managing quality and checking specifications (including centrifugal (coalescing) separators and microfiltration that you all are going on about). The important thing to understand is that the supply chain QC checks take place in a controlled environment. Aircraft already have filter screens against gross physical contamination. Moving water filtration systems to a aircraft is a complete non-starter because:
1) it moves the quality control operation to an uncontrolled environment
2) it adds weight and fuel burn to the aircraft (have you ever SEEN the kit that is used? weighs about half a tonne)
Facet vertical coalescer separators, API-1581, Category C, Type S, Fifth Edition, aviation fuel filtration applications | CLARCOR
3) You would have difficulty inspecting and changing filters safely and inevitably it would get forgotten until, oops
4) The cost of miniaturizing the components would be astronomical
Forget it.
And yes water in fuel systems is inevitable because of the continual ingress of air through the vent which has moisture in it and no its not just a problem at sea level, all air has moisture in it which then freezes and condenses on the inside skin and forms free water which then dribbles down to the bootom of the tank and gets reabsorbed into the fuel in an free water:dissolved water equilibrium situation depending on temperature / density of the bulk fuel .
And in any case who said water was the issue?
Smilin_Ed no, the tests were not done with the actual samples (there is not enough of it) so they faked up a test batch. That didnt reproduce the problems. So they actually injected water into the fuel and eventually managed to get ice rime buiding up on the inside of hoses and on the FOHE plate.