Honestly its probably too late for them to add a customisation system to skills this close to Stormblood if it isn't already planned. Its only about 4 months away. Its also unlikely for them to add such a system during the patch cycle so the earliest we would be likely to see such a system added, if it isn't already planned, would be in 5.0 in about 2 years.

As for if we should have it, I don't see it as likely. Skill customisation is generally rather questionable as far as value goes as it makes balance more difficult and adds a questionable amount of value. In the end there usually ends up as a 'right' build which everyone is expected to follow. Even in a situation where you might want to use different builds in different fights it just means each fight has a 'right' build and people will be criticized if they deviate from it in group content. Plus switching builds every fight would likely become annoying for a lot of players.

Even with the existing PvP system, the customisation is mostly cosmetic. There are places where points are clearly more valuable than others and as you level up the amount of options you don't have becomes smaller and smaller.