Prothean would make a good deal of sense, actually. The Protheans didn't stand a chance at resistance because they were taken completely by surprise. The genocide, however, took a long time. It's not entirely unthinkable that, similar to the Protheans on Virmire, others were hiding elsewhere, developing weapons. I'm just saying.
The only reason Virmire got left alone was because it wasn't in the Citadel database, and the Reapers didn't know about it. I don't remember why though... some political in fighting made the Mass Relay research kind of a hot button topic, I guess?
Even if a super weapon was under development, the Reapers would have found it, and destroyed it, at the very least, maybe even adapted against it. The only way around this is if the planet in question was off the star maps, like Virmire, and I can't see how it would be.