If they released, say, two primals in the same timeframe, then it would make sense that the weapons were comparable in power. This was the case with Moogle and Ifrit: you could have picked ACC or ATK (nevermind that ACC was a junk stat at the time).

But Ifrit and Moogle were 2011 models. Come 2012, the new models should distance themselves from the old more than being a mere alternative or sidegrade. Second Lieutenant and Garuda are comparable in power amongst themselves, but better than Ifrit and Moogle. At the same time, Ifrit and Moogle have alternative value in the form of GC seals, which you can then invest into purchasing an SL weapon. This trend should continue as new content is released.