If you want an example of a game where highest doesn't necessarily equal best, it's FFXI back at lvl 75 cap. FFXIV is far from that way. Any full ilvl 90 set (assuming you are acc capped) is going to perform within a few dps of any other combination of ilvl 90 gear. The impact on secondary stats is so minimal that it doesn't matter what you pick, you will still be doing the same damage. The fact that a class only has one main stat for damage and that all the gear with the same ilvl is going to have the same main stat value makes any kind of customization pointless.
The only way customization is anything but a placebo is if the secondary stats can compete with main stats and if there are enough ways to maximize a secondary stat without sacrificing the main stat. The only real way that works is if gear doesn't have a universal stat minimum dependent on item level and if there are more than 4 choices of secondary stats, one of which is mandatory to cap effectively leaving 3 choices and preferably more than one main stat that the class is dependent on.