..Keniclius's backstory is hard to reconcile. He's a product of the Eugenics Wars in the 1990s, and yet his plans called for spreading supermen across the galaxy? How did he even get out into space? And the chronology is screwy -- at one moment, Keniclius reveals knowledge of "the galactic wars" and the Klingons and Romulans, but in the next, Kirk is saying he's been out of touch for 200 years.
I don't think the homework was too badly done... Nobody says the first Keniclius traveled to the stars, back in the 20th or 21st century. He's only stated to have disappeared - after having been found to be dabbling in cloning processes. No need for him to hijack another DY ship in the 1990s and follow hot on the heels of Khan Singh!
Quite possibly it was his first or second clone who first traveled to the stars in the ENT era, after having shared some history with mankind. This history would thus include the first clashes with Klingons, Romulans and Kzinti (Xindi?), as specified, but not the alliances that would give the galaxy the peacekeeping force that Keniclius thought was lacking. (And note that he expressed these thoughts in his "latter essays", not necessarily back when the original Doctor was still Earth-bound...)
Or then this clone might have left Earth a tad earlier, and heard of the Klingon, Romulan and Kzinti (Xindi?) troubles through intermediates. No matter what the truth, Kirk might assume this second case because he would be aware that the Doctor had originally disappeared 200 years prior to the episode and would be thinking in those overall terms.
I had forgotten how the episode features the return of the stun setting for the ship's phasers. Nice to see the Kzinti referred again, too. And animated plants are a cute concept in an animated episode... My vote goes for "TIF" despite the rather superfluous size fetish thing.