The 'save up for bigger waves if few targets' logic is intended to compensate for the degree to which you can fortify a single whipping boy system with things like mines, fortresses, Zenith Trader goodies, Spire Cities, and the Mod Forts rewarded from nebulas.
Personally, I still go for a single whipping boy (usually my homeworld because MOAR SALVAGE), but that rule is definitely punishing me for doing so, and that's entirely fair. I think if there's only a single wave target the multiplier goes all the way up to 3x normal, now (it was 2x but that wasn't enough).
Really sucks getting waves that rarely, though, because you don't get feedback as often on how much the AIP increases are boosting the wave sizes.
Also, that mechanic could certainly be a heck of a lot more clear to the player.