I was going to make several characters and then divide the different questlines between them.
But I've only made two characters, an Imperial male that plays through almost anything and an Altmer male for the Dark Brotherhood.
One of the reasons why the Imperial does all the quests is because a certain quest forces you to join some of the factions in order to complete it, another is that my brother did it this way and I thought, why the hell not.
So my first character is now in the process of playing through all of the factions except the DB. Since Skyrim is ridiculously easy I've had no problem with making him a jack of all trades and master of ALL. I would recommend you to stick with your plan to create different characters for different factions and/or playstyles, as I think it's much more fun to play different characters who do different stuff than having one character that does everything and is a master of everything.
After I'm done with the Altmer character I'll have plans to create a character - a Nord female - who'll participate in Operation Put Ulfric on the Throne (as opposed to Operation Deliver Ulfric's Head on a Plate to the Imperial City, which the Imperial male participated in). I was gonna leave the Companions to this character but like I said, my Imperial decided to complete everything in sight, and so I started this questline this month.
I do have other characters planned - a Dunmer who fights for the memory of Resdayn and the Dwemer, wears Dwemer armor and does all things Dwemer; an Orc who lives in Orc strongholds and avoids civilization; and a Redguard adventurer who travels light, fights without armor and carves down his enemies with his scimitar.
I don't know if any of these characters will ever see the light of day, though.
But well, there you have it. My rambling account on my characters.
Oh, and about the main quest: I have never played through a TES main quest twice. I've only played one character in Morrowind, in Oblivion I avoided it because of those damned Oblivion Gates, and in Skyrim I've avoided it on my Altmer because of those damned dragons that can swoop down at any time.
Step 1. Make a mage
Step 2. Level destruction and conjuration.
Step 3. Find a pathetic, poorly defended, dirt-smeared village with quests for me.
Step 4. BURN THOSE PITIFUL INSECTS!!! THEIR LIVES AND HOMES ARE BUT KINDLING FOR MY AWESOME POWERRRRR!!!
Step 5. Raise their charred corpses as my undead slaves.
Step 6. Level up and find a slightly less poorly defended village.
Step 7. See Step 4.
Haymon Camoran, is that you?