As a 50 Marksman Sniper, I find them to be pretty equal, though since all of Scorpio's gear is moddable, i have been able to get her better stats, and she tends to get into melee alot more reliably (techstaff FTW) than Kaliyo, so it helps with her predicability.
I find myself having to help them tank, with the ballistic shield and smoke grenade. If they were equal geared, I think they take damage equally well. Their ability lists are nearly identical. I find that turning off some of the abilities helps them more reliably use the ones I want. I think that they need to decrease the cooldown on the defensive bubble they get though, 2 minutes is too long. I think 1 minute would be better.