Substituting 1 currency for another really accomplishes nothing but shifts or eliminates the burden. Paying, instead of a very valuable currency (gil), in free company points (almost worthless) detracts from the whole payment thing entirely. The developers have in mind how much player should have to work to obtain a house or FC house. By shifting the currency, you do not change the underlying amount of work the developers want you to do before you can buy a house. So, if we change to a FC points, you would have to expect to pay around a billion of them before you could get a small house.

Now, if we're going to be sensible, and we want to give FC points more use, how about we have FC points in addition to gil. That way there is a collaboration of wealth and effort on the FC as a whole necessary.