Right now the only two really relevant MMOs are WoW and FFXIV, imo. You've got some niche games like ESO and Secret World Legends (which I also enjoy), but for the most parts it's the former two that are considered the more popular ones. Here are my thoughts:
Combat: Combat is a preference, but I'll take the higher GCD and weaving of oGCDs of FFXIV anyday over the 4 button rotations WoW gives you now, even with the lower GCD (especially considering most things are on GCD now). FFXIV combat feels much more satisfying and rewards good play.
Crafting: Gotta give this to FFXIV. The crafting system, while grindy and a bit unwieldy unless you omnicraft, is actually useful (WoW crafting has turned to garbage). Weapons and armor are relevant and not immediately inferior to quest items and the job system really lets you craft items for other jobs, which helps with leveling.
Innovation: WoW wins this. FFXIV is static. Even "new ideas" like Eureka is just a rehashed versions of Diadem, which was pretty universally hated. WoW is always trying new things. They don't always work out (the new Island Expeditions and Warfronts haven't been all that well received, especially with how buggy the game has been), but they at least try something new. Raid tiers and mythic + dungeons also provide a lot of midcore content that FFXIV lacks.
Choice: Not story choice, but gameplay choice. WoW wins here as well. Talent trees let you customize your character like you want and while not always equal and there are clear winners at times, for the most part the talents are well-balanced with each other. Some are better for dunegons, some are better for soloing, some are better for raid bosses. Some complete change up play style. But that choice is there. The only choice you make in FFXIV is what job you want to grind next. There's no customization outside of that and even within job types (melee, caster, ranged), they play fairly similarly.
World-Building: I'd also give this to WoW. WoW has had time to build the world they have now, true, but even the beginning two original continents felt expansive and connected. All the zones really have their own personality and the freedom of movement around them, from flying through trees and over mountains to swimming to the bottom of the large beds of water, feels alive. There's a ton of beautiful architecture and scenery. You don't get that a lot with FFXIV with it's smaller zones and every piece instanced. To be fair, though, not many games have actually replicated WoWs scope when it comes to building the geography. WoW is pretty unique and in my mind is the best built world in MMOs. I feel WoW has also had a lot more world building in general. FFXIV is no slouch either, but WoW has such a rich history of lore that it's hard to match.
Content: Extraneous stuff not related to the main story- side quests, extras, fun sfuff to do, etc. FFXIV has housing and many items to decorate them with (a huge plus), the Gold Saucer with mini-games, chocobo racing, triple triad and chocobo racing. Custom deliveries each week. Not much else. WoW has no housing (boo), has pet battles, a ton more stuff to collect, and much, much better seasonal events, even if they could use a new coat of paint. So, this is pretty much a wash, imo. Housing does make me lean a bit more towards FFXIV, but that's a personal preference.
Anyway, I know it was a long read, but those are my feelings. Though FFXIV is my main MMO, I'd have to give the edge to WoW just because the lore building is so much better and there's more gameplay choice.