My suggestion:
PvE:
When expansion starts and we have the first tier, have a base tier be bought from vendors for Justice points earned from Heroic Dungeons, LFR and M0 which is all the same iLvl and everything but Rings, Trinkets, Weapons and Offhand is bought. Those are dropped from bosses doing those specific difficulties.
Tier 1 is bought with Valor points earned from Normal / Heroic / Mythic raids or M+ 1 and higher. Harder difficulties earned more Valor points. Can spend points to buy Tier 1 gear from vendors except Rings, Trinkets, Weapons and Offhands. Those only drop from bosses in the specific content.
Once purchased from a vendor, use Valor points to upgrade the gear to higher ranks up to a specific iLvl to do harder content. So if you only do Normal Raids or M+ like 1 - 5 for example, you have a iLvl cap you can hit. To increase the cap, must complete a Heroic Raid or higher M+. Doing so hits the next iLvl cap which you can do to do the next rank of difficultly.
If you only do M+, the caps are broken down based on the key and will eventually equal same iLvl as Mythic Raids. So M+ 1 - 5 will end up being equal to Normal Raids at M+5, M+ 6 - 10 will equal heroic iLvl at M+10, M+ 11 - 15 will equal Mythic iLvl at M+15. Cap stops at the current Tier.
The gear the drops from bosses from raids can’t be upgraded but the M+ versions can be upgraded up to the current cap for the range and then would need to get the next range to drop at that point.
Then once the next raid tier comes up, Tier 1 is bought with Justice Points, Tier 0 is bought with gold from vendors. New tier is bought with Valor points earned same way as above and all points are reset when the new tier comes out by converting Valor Points to Justice Points.
Next tier has a new iLvl range and cap and you would need to start by buying the gear from the vendors for Valor Points as before and getting the drop for the other slots from bosses to then upgrade.
PvP:
Get a complete Tier 0 or base gear for all slots bought from vendors with gold, next Tier is bought with Honor Points, last tier with Conquest points. As a new tier comes up, the Tier that was bought with honor changes to gold, Conquest to Honor and the new tier with Conquest.
Lastly make PvE gear useless in PvP by disabling effects, lowering stats or adding PvP only stats to PvP gear. Same with PvP gear, disable effects / lower stats when used in PvE content.
Will need to tweak the M+ keys for upgrades, and numbers tweak for costs, but something similar to the above would be an improvement I feel.