My personal take is that they princesses didn't want to have all their eggs in one basket, so to speak, so Celestia and Luna decided to take watch in shifts. I mean, they have to sleep at some point, and it has the bonus of keeping at least one princess available at all times in case one gets taken out somehow. I mean, yeah, Luna didn't show up until after the fact, but let's face it, the whole issue got resolved pretty quickly after Chrysalis revealed herself. I don't think more than a few hours passed between Chrysalis casting off the disguise, and Cadance and SA blasting her. Given that Luna probably isn't in Canterlot at all, and it's doubtful that anypony managed to get out of the city, it isn't that surprising that she didn't show up.
Also, keep in mind that both Luna and Celestia are totally unaware of the fact that 1. Cadance is a fake, and 2. SA is being mindcontrolled. They probably assumed something like "hey, both Celestia and Luna don't need to be around because we have another alicorn princess as well as one of the army's best unicorns around for backup". Celestia and Luna might not have ever thought that they'd need to fight one on one, assuming that "one princess + Cadance + Shining Armor" would be enough firepower to handle most threats. Heck, that makes Chrysalis' plan even better; not only does she fly under the radar but she neutralizes two rather large threats to any invasion.
edited 2nd Nov '12 10:32:57 AM by JapaneseTeeth