It's not possible that an amateur modder can match the amount of work that can be done by a professional design team so mmo modding will depend to a great deal upon automation and player-created content.
The Patent Office is a feature that harnesses player inventiveness to have people create new features for your virtual world.
It needs to be pretty limited and it needs to be manually moderated. Still, checking whether a Goblin Wall Destruction Engine breaks your game is quicker and easier than designing one yourself.
What is elegant is that designer laziness is a feature. In common with a lot of sandbox elements players love having control of aspects of the virtual world themselves even if the way you've implemented it as a designer is by being too lazy or time-contrained to just do the damn work.
Who can file a patent?
Limited by class. There will be some sort of engineer or architect class in the game, this will be one of their unique perks.
How much does it cost?
A lot. It should be a guild or factional effort to get a patent. Looking for backers and investors will be part of the gameplay of people who want to invent things (and might be pretty fun in and of itself).
How often can it be done?
Restricted. Maybe one per week max.
What happens when one of these player-created machines breaks your game?
QP is a competitive pve game like a football game that takes 3 months to finish. It's not the end of the world if an inventor breaks the game, it will just be a feature you don't roll out to other servers.
What happens when one of these player-created machines improves your game?
It will become a game option. Perhaps an option for faction leaders to chose to enable for their kingdom (do I want a kingdom that can build siege engines or a kingdom that can build warg cavalry?). Possibly something as simple as adding the Goblin Wall Destruction Engine to the Engineer's schematic set.
Can people name these after players?
Hell yeah. I know I wouldn't fork out a million gold to finance one unless they agreed it was going to be called Stabs' Goblin Wall Destruction Machine.
A player will design the suggested gameplay effect and building cost. So the Machine might take 200 Wood, 200 Iron and 50 Leather to build, be an unmanned but attackable raid accessory, be repairable on the fly by Engineers and subtract 20 from the defence of all mobs in a Tier 2 raid. I'd like them to also be able to design the look of it in some kind of editor. As a minimum some kind of concept art would be required even if it's just a photoshop of something the player Googled.
Designers have a week after it's submitted to check it balance it and ok it for production. So we might decide for this that it's not in line with the resource cost of similar machines or that 20 is too strong a debuff.
QA will be brief. The real QA consists of seeing how it performs for the rest of campaign. Forum whining will provide genuine insight into its power level much as I'm loathe to make this game yet another whine-driven MMO.
If it fits then great. Not only have you got players to do for free what most studios pay designers for you've also given people the best world ever simply because they have control over such things. Gotta love the sandbox business model :-)