You could limit yourself to joining just one of the guilds with each play through.
I did this and i'm probaby not going to play Skyrim until next year when DLC comes out or mods come out that reshape the game entirely.
The reason for this is because of the fact that i've burned through all of Skyrim's dungeons. And at the end of the day, that is probably the most of what Skyrim has to offer.
So instead of limiting factions, i'd consider limiting the amount of dungeons you explore on each playthrough. The reason I say this is because they all feel really unique. If you've explored every dungeon and on you're on your second play-through, the dungeon you're in may feel new but it only takes a particular room to just give you that "Oh I remember what happens in here," type of feeling -- its a similar feeling to Morrowind except Morrowind's caves were less detailed, and had similar structures, making the memory cloudy at some points.
Obviously if you've already blasted through all of Skyrim's caves, forts, tombs and dungeons, the only thing I can suggest is perhaps playing on a harder difficulty, so you still kinda feel like you're being rewarded when you complete it.