What makes you think he was home alone? There's not much indication where he is, and he's not exactly elementary age, either (junior high at least by the third season). Assuming, as I do, that she left him someplace that is, well, as safe as any place in Eureka's town limits (which seems to never be very safe, but people seem to make it work), in the care of someone competent enough to deal with whatever issues a brilliant quiet kid might cause, there's no point to mentioning him. Not really, anyway, when there's all of the other insanity in Jack's life. Think about it: the show is primarily Jack's story, and he spent season 3 a) dealing with having another woman in his life, b) dealing with the fact that Allison was pregnant by his one-time rival, c) dealing with Zoe going off to college sooner than he expected, d) dealing with his slightly insane sister, e) dealing with the regular antics of Eureka, and f) let's not forget dealing with Eva Thorne and with subsequently being fired and rehired. Kevin is not high on Jack's priority list under those circumstances, so we can assume that Allison simply learned a thing or two about keeping him safe from the regular town antics, so that she doesn't need to freak out about it whenever the town does blow up. It became more important again in Season 4 because of the new timeline and his lack of autism, coupled with the kindling of Jack and Allison's romantic relationship that makes Jack spend more time with her kids. So yeah, it was probably on purpose, and integrating her pregnancy was probably just a convenient means of dealing with it (it's much easier than hiding it, as evidenced by the other shows that have tried both maneuvers).
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