When you look at most Empyrean weapons they look as if they've been taken from some other game and dropped into FFXI. In my opinion most of them don't fit in with FFXIs style like Relics and Mythics do. If you look at the group pictures of Relics, Mythics and Empyreans on wiki you can see the difference, they look flashy but something's a little off. Relics and Mythics not only look better designed for FFXI, but have statistical benefits unique to their own weapon type, not just "Occasionally deals double damage." on them all; although they do have that hidden effect. Relics and Mythics can dramatically change how you play a job, Empyreans can dramatically change your damage output for that job and that's about it.

Good examples of job changing weapons would be:

Yagrush - Permanent AoE on all -na spells including Erase is unbelievably helpful at making you more efficient on White Mage.

Laevateinn - The Lv.90 version of this has +50 MAB, that's a jump of +10 MAB every 5 levels from Lv.75. While this might still be out done by Magian trial staves, it's still only Lv.90 and I suspect at Lv.95~99 this will have at least +70 MAB and will be the best staff for Black Mage, not only dealing the most damage but saving inventory space.

Carnwenhan and Gjallarhorn - Increased song duration can free up a lot of time for a Bard to help support in other ways such as curing and removing status effects. This can take a lot of stress off of a White Mage or whoever you have healing at the time. Also paired with Gjallarhorn, you can extend the duration at Lv.90 to around 5 minutes or more without the help of Troubadour. Of course Gjallarhorn, before everyone was brainwashed by Abysseas' massive MP Boosts and Refresh Atmas was essential at keeping your White Mage and other mages MP pools filled over long duration battles. Let's just hope fights like we've had at Lv.75 are back at Lv.99, very preferably outside of Abyssea.

Apocalypse - Probably the best Aftermath any Melee could wish for, HP drain and Haste. The weapon skill Catastrophe itself drains HP from the target based on damage dealt, which at Lv.90 gets at least a +25% damage boost. This for Dark Knight makes it possible to stay alive easily and Dark Knight can also become a possible "Tanking" option, even when using the Job Ability Souleater. Of course the HP drain from Catastrophe and its Aftermath healing yourself for 1000 HP+ over a few seconds relieves a lot of stress on a White Mage or again whoever is curing at the time.

Annihilator - Coronach might not be the most powerful weapon skill at the moment for Ranger but it's aftermath is very helpful, even at dealing more damage. The weapon skill itself has reduced enmity to the equivalent of having fired a single shot instead of blasting out 1500+ damage weapon skill at the target, which you are likely to do on the Lv.90 version anyway. This makes it so a Ranger can almost continuously fire shots at the target without getting its attention, making it easier on whoever has "Hate" at the time and even less stress on other support jobs.

Also in future I think that these Empyrean weapon skills will be available to all weapons, just like Mythic weapon skills are obtainable via quests, these might be obtainable via Magian trials to come or more quests. One last thing I'd like to point out is that most Relic and Mythic weapon skills have unique animations, where as most Empyrean weapon skills are older weapon skill animations with new flashy effects.