Using mA current instead of nA current can surely help analyzing circuits faster. I am not aware of the history of the ion-beams as to why other companies did not use higher current before. One hurdle that i can think of is higher charge interaction thus loss in resolution.
3-D chip makers can now accelerate their development efforts with FEI's new Vion too, according to Fraunhofer, the European research lab that is developing advanced chip stacks. MEMS devices, which also work on the micron-scale, should be able to benefit from quicker metrology and characterization.