I think something cool that you can do that I haven't seen any other server have is custom or new professions. I think this post might be a little long but the original post did say explain in detail, but I don't think it could be that difficult if you use what is already in the game. Here are a couple of ways and examples of what might be a way to making custom professions or adding to existing professions.
One possibility is some sort of mysticism/energy class, I know it sounds stupid but hear me out. First instead of having the profession go from lvl 1-525 like current professions do just have 5 simple levels, so you don't have to literally create a new skill. anything with a * is for some randomly named new item.
Level 1 Scribe:
One thing you might be able to do is combine old materials such as jungle stone, with some new dust using the upgrade stone ability maybe in a tab on the magic stone or just the stone itself. Here are a couple skills available at level 1.
Create Basin stone: 3 Jungle stones + 2 *Mystic Dust*----> 1 Basin Stone + 1 Level 1 Mystic token
Craft Weapon Shard II: 3 Weapon Shard I + 2 *Mystic Dust* ---> 1 Weapon Shard II + 1 level 1 Mystic Token
Create Temple stone: 5 Basin stones + 3 *Mystic Dust* -----> 2 Temple stones + 2 Level 1 Mystic Token
Craft Wep Shard III: 5 Wep Shard II + 3*Mystic Dust* ----> 2 Wep Shard II + 2 Level 1 Mystic Token
Once enough of of the profession level one tokens are collected maybe 50 you can create a level 2 profession token .
Level 2 Apprentice:
Levels 2-5 will require the appropriate level token and will give them more of the same token as to level up.
Create Fire stone: 3 Temple stones + 2 *Sacred Dust* + 1 level 2 Mystic Token----> 1 Fire Stone + 2 Level 2 Mystic token
Craft Weapon Shard IV: 3 Weapon Shard III + 2 *Sacred Dust* + 1 level 2 Mystic Token ---> 1 Weapon Shard IV + 2 level 2 Mystic Token
Create Shadow stone: 5 Fire stones + 3 *Sacred Dust* + 2 level 2 Mystic Token -----> 2 Shadow stones + 5 Level 2 Mystic Token
Craft Wep Shard V: 5 Wep Shard IV + 3*Sacred Dust* + 2 level 2 Mystic Token ----> 2 Wep Shard V + 5 Level 2 Mystic Token
As you can see the pattern forming you can also create combinations for levels 4 and 5 that are more difficult to get such as unbound energy, fine iron and mystery shards.
One possible way to obtain the new materials such as sacred dust and mystic dust etc. would be to add them into game objects and have them scattered around like in Fantasy jungle. The bonus with game objects is that if you dont like the energy theme there are a lot of options. Another way to get these items might be from existing professions such as fishing spots located inside the Custom instances, disenchanting custom items or prospecting deathwing shards. One bonus about using prospecting and disenchanting is that many players already have those professions maxed.
If it seems like too much work and adding new items replace the *Mystic Dust* with like deathwing armor shard since there are already 5 tiers to those.
I think this might give some class another way to help progress past some of the dungeons not suited for their class, such as ranged and caster classes or just give players a way to clear all of the old materials just gathering dust in their bags.
If upgrading the materials seems to overpowered though you could use the same system but to create things like bags, or alternate gear pieces, not necessarily overpowered (even +50 str is better than no str) but stat bags maybe with limited space so players have to chose stats or bag slots. Or some of the bags could have only 1 particular stat with unique equip so players need to chose which bags they want either secondary or main stats.
Sorry if my post is too long but its something new, not just another instance, gear piece, vip/vote thing, or pvp area and it is a Mega Suggestion :P