What is already out there:
In Mount and Blade their were a group of companion characters which I found very interesting. You needed to find them at different locations and have sufficient money and leadership skills to convince them to join your group. Once they joined you could give them any equipment you desired. As they leveled you could choose how to distribute their skill points. They were interesting, when you ventured near their hometown they would give you a little back story about themselves or the town. If their morale fell they would complain about certain other members of your party or reversely compliment certain others. If their morale fell too low they would leave your group taking any equipment you gave them with them. Eventually you might be able to find them again somewhere new.
The game oblivion included a little mini-game in which you could try complimenting, joking, intimidating, or something else I don't remember, to get NPCs to like you. This was important for obtaining quest information or getting better deals from merchants, there were also numerous escort quests like so many games at one point they also had follower characters such as a mercenary that could follow a few basic instructions (attack with magic/attack with melee/etc.) similar to pets in many games.
There are several MMO games out currently that allow you to level specific character skills while offline through the use of "jobs" (I believe EVE online, and City of Heroes are a couple of examples of this). Mortal Online has passive learning skills "skills learned by studying a book" or similar but only while online.
Another interesting game in development, the Secret World, has had different puzzles revealing tidbits of information (Mortal Online did a bit of this as well with their timer background images). Its just another example of offline gameplay that could be looked at.
A Tiered Game Structure
To make a game like this work I think it would need to be developed from the start as two separate but integrated games, each with their own appeal. Each portion could conceivably stand alone, what you did in one could effect the other but you would not necessarily have to play both if only one style of game play interested you.
The browser portion alone would be free possibly with advertisements or a bonus coin shop (idk) but could give you access only to semi-intelligent mobs (goblins, orcs, sator, tengu, etc.). As your mob grew more powerful you could distribute skill points: specialize in a specific weapons, work on defense through armor or evasion, work on stealth, develop the ability to command other mobs (these would be in limited supply, so another player with a higher leadership skill could possibly steal your minions away from you). You could order your mob to any area of your choosing. An intelligence stat might control how many orders you can give to or reports you can receive from your mob.
The benefit of all this for the MMO player paying a subscription fee, is first off more intelligent, less predictable mobs. When combined with the NPC companion system the two games really become one. I imagine a few different types and levels of companions:
1. Your AFK player character and alts - this could have a slow leveling job curve. You would need to spend actual time resting and feeding your character. Reading a book would take time (possibly based on a reading skill); or pay a teacher character to train you, instead of the classic you have been trained +1 swordsmanship instant pop-up message, your character would be training in a dojo. The thing to consider though is that while some areas will be relatively safe because of guards, the way I envision it no where would be completely safe. You have to be aware that some of the logged in characters will take great delight in killing your automated character. I would imagine Assasin builds could be much more literal in their purpose.
2.Companions - these would be like the Mount and Blade guys. You could equip them as you please, give them basic orders, perhaps even edit what they say as greetings to players they like or dislike or when attacked or killed. Their loyalty and how many you could retain would be based on your player characters leadership skill combined with your followers morale. They would do the same type of jobs player characters did while afk; craft a thousand swords, fish, eat, or sleep, mine, build housing, mind a store. Things could get even more interesting if you were able to hire them out or do services for your guild.
3.Associates - These would be guys who would do things for you, but are not your followers. For example you might bribe a guard to let all of your guild members pass by without inspection and alert your account and guild when an enemy guild or player shows up. He might except some weapons from you but would only use what was deemed appropriate for a guard. Another example might be shop keeper or other dedicated professional. They will work for you but only at what they do, selling, mining, fishing, etc. These guys could also have morale, or vices that require careful management to keep them from ripping you off. Other players with more money or higher Charisma might also be able to steal them from you.
and of course finally the Mobs
Some of their behaviors could be guild based. Mobs would attack all humans, but human automated characters could be given different orders based on if a guild were their own, marked as allied or marked as enemy. To make this more interesting guild identifiers could be made more complicated and they could fall into one of two categories overt or covert. Overt guild identifiers could include things like banners, embossed shields, signet rings or seals. These however could be looted. Covert guild identifiers could work like an emote that requires the player to be online. These could also be compromised by an enemy player with a spying skill and then a refreshed covert signal or password would have to be desiminated to the guild.
Keeping the Balance and Fun
For a game like this to succeed both parts would need to be fun and entertaining, and neither could be seen as "ruining it" for the other. This would be despite part of the fun in both halves would be precisely "ruining it" for the others. Watching some automated character going through a repetitive task as he levels his whatever skill, chopping off their head and disappearing into the shadows of the rafters as more automated guards run about searching for you - fun. Figuring out a prime location to drag an entire pack of mobs, influencing battles watching enemy guilds fall prey to an army of goblins- more fun.
Balance is tricky. I think mobs should not be able to distinguish human guilds. Mobs and Associates should be on Perma-death. Companion to leadership skill points should be a very low ratio. Alts should be limited.
Managing Associates and Companions should be a tricky buisness. They should have personalities, take offense to certain things dialogue options or other associates, steal, or wander off and get drunk.
Thats all for now.