I think there should be two end-game gearing systems. One for PvE and one for PvP. Both would be based on exchanging points for items, and upgrading items with points.
Doing PvP content would award you with 'Glory Points'. These could be exchange for PvP items at NPC, and also upgraded to higher tier with points. These items would be best for PvP. They could also be used for PvE, but they would be slightly worse for that. Perhaps there could be a PvP only stat that increases your power significantly when fighting against other players. And then the normal PvE stats on these items would be slightly lower than their PvE counterparts. This way PvP items could still be used for any content; however, they would not be the absolutely best pick for PvE content.
'Glory Points' would be earned by doing open-world PvP (each killed player only granting certain amount of points once per 30minutes), by doing arenas, and by doing battlegrounds. There would be a weekly cap on how many points you can earn.
Doing PvE content would reward 'Prestige Points'. These could be exchange for PvE items at NPC, and also upgraded to higher tier with points. These items would be the best for all PvE content, but not so good for PvP as they would not have that special PvP stat on them.
'Prestige Points' would be earned by doing quests, killing world bosses, and for completing various world events. Higher amount of points would be rewarded for completing dungeons and raids. There would be a weekly cap on how many points you can earn.
There would also be a weekly cap on how high each item can be upgraded to. Akin to 'item level' in WoW. So let's say that on Launch of the game the max item level upgrade would be 100. Then after 3 months, each week the cap would be increased by 4 item levels so 16 item levels per month. This would increase for 3 months for the total of additional 48 item levels so bringing the max item level to 148. After this, for the next 3 months there would be no increase, and after those last 3 months the first season would end. Each season would last 9 months in total, and every 9 months a new season would start along a new big patch to the game with new dungeons/raid/quests and other activities to do. Each season you would keep your character and its progress but all items in the game would be reset back to item level 75 or so if they were higher than that. They would be labelled as 'Season 1' items, and they would not be upgradeable anymore, but they would be a very good entry point for doing the end-game content again in the new season. The 'Season 1' items would also be useable on your alts, scaling with the level of the alt character similar to heirloom items in WoW. So every season you could start a new character and have a set of items that will take you to max level without worrying about getting items while leveling up.
There would also be ranking each season, and you could also check the ranking for past seasons. The ranking would be for dungeons, raids, guilds, completed quests, gathered gold, crafted items, damage dealt, heals done, etc. Every player could find something for themselves that they want to excel at in each season. There could also be special awards for reaching certain ranking points in each ranking.