Actually I have a solution to just about all these issues. Sigh I'll never get to make my games so I might as well mention a few here.
SELF PERPETUAL CONTENT is the important thing and all MMORPGS should be centered on it (can't say it loud enough). MMORPGs content may be vast but what's around the corner is predictable and developers could not possibly add content quickly enough for a truly evolving world. To this end more game play ideas need to be player driven. I suggest...
Quests for items of power: Every rpg around has the player collecting things for a climatic conclusion at the end of the game (orbs, elements , etc.). Why not have multiple items of power for players to collect in a MMORPG.
1. Each would spawn in pieces at random but spaced out points and require collecting.
2. Bearers of a piece would be open to pvp combat from anyone and be able to detect which direction a piece is in (think highlander).
3. Knowing a person has a piece could only be determined by holding a piece yourself or a rare item (and even then only give you a direction). The game itself would allow killing players anytime but attacking a player without a piece would give you a very stiff penalty.
4. Collecting all the pieces would in essence make you a boss level character (requiring multiple people to take you down) and allow you to put a useful buff on your followers. This means people would both flock to join your group/clan for the buff and flock to attack you for your item of power.
5. Defeating a holder of an item of power would only get you one piece of it the rest would respawn in the world again to be collected.
6. You could also only hold an item of power for a limited time before needing to visit that item's "place of power" to renew it or it would be automatically respawned again. Of course rival groups will try to take it from you when you try and renew it giving another reason for guild vs. guild combat.
I've got other rules too but it's too long to get into (like you can't hold two items of power, be double buffed by items of power, preventions for log out running and holders of items of power are damaged by each other automatically in close proximity preventing team ups).
Game Masters: Find honorable players and reward them with a free account if they become game masters. They would be much more than just admins they would have the ability to create simple custom quest sequences. Creation would be pretty simple add NPC at xy coordinates, with custom text, add destination point, spawn monster/item at destination point if you've talked to the NPC, give reward to player on monster defeat or item retrieve, etc. It's seems like it would be ridiculously simple and easy to implement and add loads of replay value. Game masters could also disguise themselves as a player of any class or name. Imagine pretending to be a newbie and rewarding those who help you. I've got a game story idea for this to fit into as well. The hardest part would be simply finding players who would not abuse the system. Note: I'd also give the ability to display banned grievers/hackers/botters avatars in medieval type cages or with their heads on pikes as an example to others...
Don't divide players: Having set groups of like horde or alliance is always going to have balance issues (on Battlefield Heroes the balance issues are horrible). Plus what if I want to hop over to the other side and play with a friend over there? I shouldn't have to re-roll a new character to do it. I much prefer player created clans and benefits should be directed to encourage them. I'm thinking stock buildings/castles could be purchased and added in game at server maintance times. Should one clan "rule" a server too much GM's could encourage the growth of others with their abilities. I can see GMs finding and empowering "champions" to slay a person with an item of power should they get to powerful. It would fit very well into the game with the story I have in mind (you know wise old sage/wizard mysteriously appears to a young hero to help him slay the darkness that rules the land).
Randomly appearing dungeons: Think of the movie Krull. Random floating castles appearing in the sky (I know Krull's didn't float) would be quite a surprise for players to suddenly find at familiar places. Other dungeon spawn types could be cracks opening in the ground, distortions in space time, giant monsters swallowing you, etc. You could even have the option for players to learn an ability to predict these spawns.
Towns being attacked: Towns are to boring. While I want some main towns to be safe places I'd like other towns to be able to be attacked at any time by hordes of NPC monsters/enemies. Imagine being in a town and hearing the church bell ring as a warning. Better get ready to defend it or it will get burnt to the ground.
Client based appearances: I've always been annoyed that no matter what you do in a MMORPG NPCs will still be doing the same thing. If a town appears half destroyed and you complete a quest to help repair it will never look repaired. This is because MMORPG makers seem to think all clients need to display the same graphics. As long as the collision meshes remain the same why not display different graphics to different players before and after completing certain quests. Furthermore why not have more NPC's only visible to players on certain quests? This would lend immensely to the illusion of a changing world.
More frequent transport spots: I don't mind long rides but most people don't have all that time to waste. Typically once you visit a town you can go there via a transport service. I'd just have more transport points along the main routes. In my story idea riffs in space time are common so you'd just have to find one once to open it for use. With all the random and custom content that can occur with my other ideas taking a walk may still be worth it sometimes though.
The main thing is these things are all player driven. A changing world where anything can happen will always be more exciting than a static one. Other things are...
No classes: Most MMORPGs determine abilities from picking a class. I'd reverse this and determine your class from what abilities you choose providing a system that you could learn any ability you want. Similar abilities would enhance each other but if you want to be a healer who wants a sword attack you could do it. You'd have a limit on how many abilities would enhance each other, like say 7, so you would encourage many duel custom classes. For example if you had a limit of 20 abilities at any given time you could have 7 healing 7 sword, 3 agility and 3 strength.
No levels: Actually I'd keep levels but just make them only minor enhancements on your stats and have a low cap on them. The real training would be on abilities. Use an ability a lot and you'd get better at it. Which abilities you have equipped would effect your stats. This way is more like real life where you get better at something from practice. I know that your may be thinking it will be boring to have to grind up an ability you only use once in a blue moon but the exp required to master one would not be a lot. It would require enough exp grinding to prevent swapping abilities quickly. Having multiple abilities would be what keeps you busy. This should encourage swapping single abilities to experiment but discourage swapping them all as it would be like re-rolling that character. You'd have a starting set of abilities but most would be earned via quests in game. I like feeling like I built my characters up not just assembled them.
Mini games for crafting: With crafting it's rather boring to put things in a slot and have to push the same button sequence over and over again. Either make each a full fledged flash level mini game or make them simple enough I can set it up to be done automatically. I can easily see Tetris, Bejeweled, Desktop Defense styled mini games used for crafting. I mean come on if Final Fantasy 7 can have Chocobo racing and breeding and Final Fantasy 8 can have a complete card game MMORPGS can do better.
FPS style MMORPGS: This would address latency issues and the game itself would not necessarily be an FPS, just set up that way server wise. It could be done if a MMORPG maker partnered with or owned a server rental service. You'd make renting a server only slightly more expensive than an account and throw in an account with every rental. Items/exp would only be accrued on official maps but with a server rental you'd have the option to run customs and choose which instance runs. Trading/LFG could be done via a web paged based master server (all of which would be themed to not take you out of the experience). Want to go a space trade run? Post you are hiring escorts, hire them, go to a server, space pirates could join and try to take your cargo. Same thing could be done in a medieval type game. Note this idea is for a different game than the others.
Billing: I don't like to buy something and feel obligated to play it. I suggest billing be done more like game rentals as in a weekly manner rather than monthly. Most people didn't have a problem with game rentals back in the day. You could buy "tokens" and each token would be worth a week of game play. After a week a token would need to be used to continue to play (with a warning before it is). If you played for a month continually the price would be the same as regular monthly fee MMORPGS but if you wanted to go on vacation it would turn off and not cost you money. Tokens could be packaged to give a discount as well if you bought more at one time.
Anyway I have a ton of other ideas all of which are libel to be used before I will get to T_T

. GTG, hope it made sense I had to post before I could check it a lot.