Actually, the armorer, while still the same, is the Miqote outside, where she's always been. The Smith master was Mimidoa (sp).

The Old Lancer and Archer masters are around, but they're not guild masters. You see Godwin from the Archers and you meet the Lancer master in his personal chambers during the Gridania story.

The Conjurer master is actually still where he's always been, the Padjal E-Sumi-Yan. I'm curious what happened to O-App-Pesi though... Also, the Botanist guild leader is still the same. The ones that have changed are:
Miners
Goldsmith
Blacksmith (Still In Game)
Marauder
Gladiator
Lancer (Still in game)
Archer (Still in game)
Thaumaturge
Pugilist
Arcanist (You visited that guild at met the master in the 1.0 story, their disappearance is a major point of the ARC story now.)
Weavers

Ones that are still there:
Botanist
Conjurer
Alchemists
Fisher

No Clue:
Culiniarian
Leatherworkers?
Carpenters (I think it's the same guy...)