I think to be guild leader you should be required to have all the applicable skills at 100, maybe even require certain perks, even after completing the quests.
I am not going to finish the last stage of those quests until I do have the skills at those levels. It just wouldn't feel right. I hope they make a mod for that.
All applicable skills at 100 would be over the top. I reckon it should work on a skill pool basis. For each rank in a guild you would need the skills for that "class" to add up to a minimum total, which gets higher with each rank.
So, to join the College of Winterhold, you'd need a total of 150 skill points across Alteration, Destruction, Conjuration, Illusion, Restoration and Enchanting. This could be reached with 75 in one skill and 15 in the rest (total 150), or with 25 in all 6 (total 150).
To rank up once, you'd need your magic skills to come to a total of 200. Then to rank up again, 250. To rank up again, 300. Eventually to become Arch-mage you'd need a total magic skill pool of 500 or so, to reflect the fact that you're actually a damn fine mage.
The numbers are obviously placeholders, as some of them might be restrictively high (500 would require 83 in four magic skills and 84 in two, or 100 in 4 and 50 in 2, and so on, which might be excessive).
Just a thought.
EDIT: on second thoughts, 450 would be about right to reach Arch-mage. That would require 75 in each magic skill, or 100 in 4 and only 25 in the remaining 2, or 50 in 3 and 100 in 3 and so on... difficult to attain, but far from impossible.
Also, it might make sense for the required skills not to necessarily be the 6 for that "class." For example it doesn't necessarily follow that all Thieves Guild members should need Speech, or even Light Armour seeing as being a thief doesn't necessarily entail getting into fights. The required skills that make up the skill pool need not necessarily be the 6 "class" skills, but as long as there's a clear set of 6 or so skills needed, I think it would work nicely.
Not 100% sure which skills would be in the Dark Brotherhood's skill pool though. Maybe you'd need to kill a certain number of people to rank up - similar to how it works now - but also you'd need to have a skill pool across all damage skills (One-handed, Two-handed, Archery, Destruction) plus a couple of indirect damage skills like Conjuration/Illusion and Sneak/Alchemy.