I've played her only three times since the release of wave 5 and lost all these games However, I was mainly experimenting with new stuff (I hadn't used the Emissary before) and can't honestly say I played her to the full potential. I also didn't use Taproot in any of these games, which was a mistake. It's probably going to be my auto take with her as it can make her and the crew much more survivable. I definitely underutilized Royal indignation , as 1 point of armor can prove essential in some situations.
Cyclops are huge and have low Df of 4 so they draw attention and take damage easily. However, they heal fairly quickly too (with a discarded ram at the start of their activation, and scheme marker from Malifaux provides it's 4 wds back per turn). I've yet to play on a table where their Ice Pillars could form a good choke point but in other circumstances they can be a nuisance too. They work really well with Zoraida too, as Nurse can easily fully heal them and they don't get paralyzed.
Emissary was a key model in all three games I played. Being able to reliably summon a solid scheme runner (who can also hit surprisingly well) or two each turn is great. I also found his trigger that discards markers a great option in some cases. His action to buff friendly Fae/place Scheme Marker came in handy too.