They haven't done particularly novel things with missions. It's all the same old deal. Talk to person, accept mission, mission goes into mission log, go kill bad guys, repeat. So naturally, I've been walking around accepting all the missions I can because, hey, why the hell not? And I've got a huge pile of missions that I really don't know much about, but I'll just go select the next one and do the next one when I feel ready.
World of Warcraft "solved" this problem by limiting the number of accepted missions you could have. I think it maxed out at 20. This didn't actually change anything - it just meant you had a text file open while playing, writing things down like "elf girl, felwood forest, 3 missions". And it meant that you couldn't just wander around and do all your missions when it was convenient - more than once I found myself saying "oh man, I have missions here! Except I don't have them in my mission list because I had that giant group of missions in Gadgetzan that I needed to free up space for and I guess I didn't get them back dammit."
Obviously, IMHO, this isn't ideal. I like the limitless mission journal. It's more realistic. I don't have to delete "learn guitar someday" when I realize I have an unexpected stop at Trader Joe's.
But then, if we have a limitless mission journal, why bother with "accept this mission"? Why have "missions offered" to begin with? Perhaps I should just walk up to someone, and he says "Oh god, they've taken my shovel, I loved that shovel, please has anyone seen my shovel" and bam, mission. He doesn't have to say "you should go find my shovel! I shall give you a reward if you do. Do you accept the mission?"
There's no mission. There's just a guy who's lost his shovel. And your character writes it down in your notebook because, hey, the guy's lost his shovel, maybe you can find it.
I find this a little cleaner, more elegant, and more engaging.