I think there's an important distinction to be made, and it goes back to what I said earlier about Sara now being the parent on a show about the kids. Klemmer didn't compare Ava to Lucille Ball; he compared Jes to Lucille Ball. The big outside-the-box talents Caity brings with her are movement-based: she's a dancer and a martial artist. But, it's very rare nowadays for the Legends to actually be able to put those to use; I don't remember any fight scenes last season other than Crisis, the finale, and the Genghis Khan episode (which Caity directed). But, one thing Caity doesn't notably bring to the table (not that she can't passably do it, but I don't think it's something for which a showrunner would say "I need Caity for this!") is being funny; it's just not one of her strengths and it's certainly nothing to do with what Caity signed up for in Arrow season 2.
Unfortunately, Legends has been written as a out-and-out comedy for several years now, so when they discover that Jes has the comedic chops Caity doesn't necessarily have, the producers are going to gravitate in that direction. The aliens plot then gives them a way to let Caity do more ass-kicking (which I think she's been asking for) while the rest of the team are having wacky hijinks.
And for the co-captains thing, the alternative is centering the show around a leader smashing a subordinate, which brings its own ration of icky. Making Ava co-captain at least heads off the most basic levels of that complaint.