So, supposing that X's tiredness is related to the echoes of history and the reawakening of tragic memories from over a hundred years ago... Did you want to venture a hypothesis on where Zero is for the other half a century where he's not being studied and worked with?
There's multiple ways we can approach this. One proposition could be that the study of Zero did not have to start immediately. We know for a fact the facility in question was built to house him. How much time was needed to build this facility?
Likewise, we could wonder if the idea of studying Zero's Sigma Virus came about immediately. Zero's initial purpose was to remove something from himself. Perhaps they spent a good portion of that time removing the thing in question? Perhaps Zero was put in quarantine for a considerable time in the hopes that his absence would stop the spreading of the Sigma Virus? Perhaps for the longest time they ignored Zero under assumption that the samples of Zero's Sigma Virus were no different than the regular Sigma Virus? We would also have to consider the trouble in properly avoiding the negative effects of Zero's Sigma Virus on the research in question. Studying the Sigma Virus under safe conditions is no small feat.
The opposite proposition is considering the effectiveness of Mother Elf. With the completion of Mother Elf, Zero is purified from the Virus and his study comes to an end. But what about the rest of the world? Was her effect an instantaneous deus ex machina or did it take nearly half a century to turn all the Mavericks to normalcy? How long does it take to eliminate the Virus once and for all? Certainly "reversal" is incomparable to "immunity", conflicts will still arise and those irregulars will have to be stopped in order to cure them.
To simplify the above even more, X did say "nearly" one hundred years. We can thus shorten the timespan that needs to be covered to considerably less. And if all that is not enough, we could start looking at the combination of both seals to account for the near hundred years in question. As you say, the first few decades of Neo Arcadia's unstable beginnings could certainly add a bit to our total. But to say the whole near century after Neo Arcadia's founding was such a conflict? It feels quite wrong to think of the utopia as never having truly known the peace Zero sealed himself away for...
But that they take such a flippant approach to fighting could be indicative that they weren't around for the hardcore Elf Wars. Where even X needed a helping hand and combat gods like Zero and Omega roamed the Earth. It doesn't seem like they've had that overwhelmingly horrific war atrocity experience firsthand, or been humbled before by truly powerful enemies as our heroes faced in the Irregular Wars, before Zero came along. Like four big fish in a small pond, before the floodwaters broke.
Harpuia does seem to have a certain innate knowledge on the powers of Baby Elves, though. Did he experience take over before, saw the grueling atrocities they can cause or is he merely basing it all on the stories he has heard of the great war? Likewise, we must consider each their attitudes to combat. Matters such as Leviathan's boredom and Fefnir's burning desire, which exist in some form in Phantom and Harpuia too.. All of that could be born from the strong enemies they've once faced and that exist no longer. As they are still undoubtedly special as X-bioroids, they might not have been humbled by power, only by inexperience. Standing grounds in Elf Wars, rising to their status as four guardians, the ones without equal, the reappearance of Zero awakens in them that long forgotten need to fight.
RTRZ booklet suggested something like that, but it's more a matter of reconciling that with what Takuya Aizu mentioned in the interview portion.
Would you happen to have some specific statements on the matter? All I have at my immediate disposal is the biographies of the Big4, do the interviews and other shed more light on the matter?
Oh and one of these days we're going to force you to translate all of RTRZ, especially that website.