Dark Depths Replaces Maze of Ith & Thespian Stage replaces so-so lands like the 2nd canopy or a cavern of souls. It's much easier to squeeze in into a non splash straight up GW list. Yes if you see a Karakas on the opposing end of the table of expecting STP, you can just stick to plan A which is to beat face. If your opponents leaves knight on the table, that usually means they don't have Swords anyway. Jace, Liliana etc are sorcery speed and don't work very well at killing Marit Lage. Kotr can deal with Karakas really easily by fetching wasteland.
As for Loyal Retainers-Fauna Shaman, yes it's way too slow for an I win condition. I think it is powercreeped by the Dark Depths combo which requires very little slots. Loyal Retainers and Elesh Norn are very often dead draws and Fauna Shaman isn't the most robust creature. You can be tuturing a few turns to set up the combo but if Loyal Retainers gets countered, you are in trouble. Also Elesh Norn is scary only in the aggro/midrange mirror. Control can deal with Elesh Norn with Jace etc.