Right now, to me it seems like a lot of areas of the game are working relatively well. How well exactly is up for discussion, but most areas could be improved merely with tweaking, better/more content, or the like (raids, dungeons/M+, WQs, etc.). Two areas stick out for me as really being have so many problems, however, that they need a top-to-bottom rework - and I would say those are Crafting, and Instanced PvP (leveling from 1-100 too, perhaps but I feel like that's less vital).
With crafting, we have a system that complex/fiddly, boring, and produces relatively low-value goods at most levels - even where it produces higher-value goods, they tend to be eclipsed by drops or even obsolete by the time they are available. Virtually every game which has crafting has a crafting system that has more point to it, and works more entertainingly than WoW. Even the few that are more tedious, like GW2, have a least a strong point to them.
Blizzard have struggled with crafting and what I'd really like to see from them is to reconsider the entire system, top-to-bottom. I would propose removing any things that could be crafted or the like, but change the way that they're crafted? Making existing stuff some kind of "legacy" tab? I think that could work.
I'm not suggesting a particular solution because I think Blizzard could probably do a lot better than anything I could come up with, but at this point, I feel like crafting is weighing WoW down, and serving almost no purpose, when it could be a fun and engaging system for filling up downtime. The crafting quests and story and so on Legion were cute, but not much else.
I'd love to see crafted items actually be sought-after beyond the first couple of weeks of the expansion, and not just to be obliterated or whatever.
Instanced PvP seems to be in an even worse state, in part because of Blizzard's hap-hazard and half-arsed attempts to turn it into a SRS ESPORT (let us pray M+ does not suffer the same fate - I suspect it probably will though). By trying to push organised PvP harder and harder, and by making PvP feel less involving and rewarding, and by sheer "battleground overload", Blizzard have made PvP into a daunting and largely unenjoyable exercise, where again, it used to be a fun way to fill up time.
First thing that needs to go where is the current PvP rank/prestige system - by all means continually reward people, but this is just a tedious grind, even by WoW standards. Look at GW2's reward tracks instead, perhaps.
Second thing that needs to go is PvP talents. Most of them are dull passives, and the active abilities often seem better-suited to PvE. Just give us a fixed suite of passives that kick on in PvP, and consider moving and re-working active abilities for maybe another tier of talents (below 100 somewhere) or two.
Third thing that needs to go is the battlegrounds. Not all of them, perhaps, but any that survive the cull need re-working, complete. Re-engineering with modern WoW, modern classes, modern abilities in mind. This would go well with a revival of HvA warfare as a concept generally. Any "legacy" ones could be kept as brawls of course - they're a fine concept, even if some of them are too dull for words.
Fourth thing that needs to go is elitism/e-sports obsession. I know a few people would be really upset about this, but PvP seems to be moving to that place raids once were - with the population dwindling gradually. Look to Blizzard's other games and see what can be done to improve PvP, matchmaking and so on from them, without trying to force everyone into large premades, because that just isn't going to happen, for the most part.
Finally, what is even the point of Warden Towers and/or FFA PvP areas? Maybe on PvP servers they work (do they?) but on PvE servers, the opposite stays STUDIOUSLY away from Warden Towers, and in FFA PvP areas, most people very carefully and cautiously avoid harming each other as they slowly farm the content. I mean, some free honor and maybe MoHes and stuff for very little effort, I guess that's nice buuuuut... C'mon, what is this? PvP should involve SOME kind of PvP man. Or at least the risk of it.
I'd also make PvP more rewarding general. I mean, unless we're abandoning the whole HvA concept (in which case fine, do nothing, but...), then PvP should be more central, more desirable. Not just a place to grind stuff in a dull fashion. A place that's fun, exciting, and has some decent rewards. Blizzard need to let go of their fear of making PvP rewarding.
Personally I'd love to see all current BGs made "legacy", and new BGs, with a strong focus on HvA as a theme, and a strong avoidance of vehicles that weren't specifically siege-weaponry, or needlessly exotic nonsense, replacing them, but I wonder if people would see that as a step too far.
Do you think any systems in WoW need top-to-bottom reworks?
(* = I imagine world PvP is even worse off, but I don't play on a PvP server so...)