Putting her 3S so late in the program would probably be the worst thing she could do, given it's the jump that gave her by far the most trouble this season.
As for Waka focusing on "transitions" to get higher GOE like Evgenia... call me a cynic, but I don't think their actual transitions into jumps are the reason causing their different scores. Look at Wakas 2A combo, which is coming out of a really difficult transition, and the relatively still stingy GOE it gets (depsite good height/ice coverage too, and being placed very well to the music - remember the roar of the crowd in Milan at that moment?). Waka doesn't get rewarded like she should be in GOE & PCS anyway right now. Not sure I'd want to trust judges suddenly rewarding me in that if I was her. Might as well go for the 3A - if she rotates it, they can't really take her BV away, and it might as well cause her GOE & PCS to go up more then actual improvements in GOE & PCS (because that's what ISU judges do

).