I'd like more guilds and I'm especially fond of the Guard faction and the idea that certain quests are only available when you're a member of multiple guilds. I'd like to add another option for guilds: Certain (non-main-)quests can have alternate endings due to new options becoming available by your guilds.
I don not like the idea of missing out certain quests to have other ones in it's place.
Also, if you join the Guard, the Thieves guild would be happy to have you - an infiltrant is always welcome.
Synergy quest example:
The guard asks you to spy on the thieves guild. However, you're also a Thieves guild member and a guild associate asks you to deliver falsified information reports. The choice what to do is still yours to make, but had you not joined the Thieves guild then you would never have had a choice.