When TES3 was being still developed, bethesda promised political games and to be able to climb up to the highest rank in a guild and then do something with it. Beth never delivered, and it's kind of pointless to be the head of something but with the power to do nothing.
This led me to start pouring out a whole bunch of ideas, whereupon I realized that it had gained the scope of a completely standalone mod that could fulfill something a lot of players have been wanting for years: a real reason to become guild head. Unfortunately, I'm not nearly good enough to accomplish this, so I'll toss it out for others to take up the torch.
This mod will require resource management! But then, as I'm sure you're all aware, becoming the head/leader/boss of any organization is more about paperwork than anything else. In this case, I'd say keep it simple and measure everything in terms of cost.
You start off with x gold (say, 100K) in operating capital. You automatically gain x gold every week from random minor jobs, donations, grants, and membership fees. Each week, you also get a mission to which you can delegate some of your guild members (or do it yourself). The missions would be broken down into four levels of difficulty, which are listed when the mission is given to you. You then decide which resources to allocate; lesser resources have a lesser chance of getting the job done right, but cost less - they're good for minor missions; likewise, something major would require a greater number and/or higher quality of people (which, of course, costs more). You can always volunteer yourself for any given mission, which costs the guild nothing, but if you fail, you die and it's game over.
If you delegate someone else to do it, it's handled behind the scenes (you get a message a few days later) and there's a random chance of success, modified by mission difficulty and the resources allocated. If it succeeds, the guild gets paid and you make a percentage. If you do it yourself, you get paid and the guild gets a percentage. If it doesn't, you lose all the money you spent. If your operating capital gets to 0, you can't take any missions and you might even have to deal with angry guildmembers (sort of like the "you got kicked out of the guild" quests). The kind of quests you get are pretty much like what we already have:
FG: Some random town/settlement is being terrorized by a big bad monster/group of monsters; someone wants to retrieve a lost item; someone wants a trophy; someone needs a bodyguard (once the assassin is dead, the mission's over).
DB: People need killed. Duh. There are a couple mods that deal with this already.
TG: Someone wants to steal/recover
MG: Find
You could also toss in some (no more than three each, I'd say) special one-time quests that pop up randomly, that would require the expertise of the guildmaster him/herself. These could be multi-stage quests, and while you're doing them, you personally can't do other jobs, but the payout is much higher:
FG: Hmm... I'm drawing a blank here. All I can think of is bigger versions of the normal FG quests.
DB: Someone needs protection (The Assassinated Man), or a particularly powerful being needs to be killed.
TG: Someone wants to steal a really well-protected item, or someone wants to find a person who's very well hidden.
MG: A rogue mage gains enough power that he becomes a threat (though whether or not he actually is, is another story - is he someone like Mannimarco, or is he simply happy to putter around in his tower making potions and someone just wants to get rid of him for his research? <_< ); someone wants to recover an item (a book, maybe) lost in an old ruin that no one knows about - you'll to do research in the AU archives to find it, then go there and get past the wards and guardians to get the item.