I think it's more a case of people imagining SIT is being skipped, because they overrate it's quality as an album.
Heaven Can Wait was on every tour until fans didn't vote for it on Ed Hunter which surprised Steve and is why it hasn't feature much since then, Wasted Years was also on most of those tours too in that period.
After that Bruce came back, and SIT was his worst album so no surprise that there was going to be less emphasis on it. It also coincided with a time period when they have a lot of material now. SIT isn't that much more overlooked than SSOASS, it's just SSOASS has more hits than SIT to choose from for the usually 1 track they get in the set, 3 tracks from SSOASS get roatated around whereas it's usually Wasted Years or nothing from SIT.
I'd argue it's more a case of 82-84 being over represented in sets than SIT being overlooked.
If this were 2006, I'd agree with you. Up until then, there was nothing particularly noticeable about SIT's representation in live setlists. But things changed with SBIT. Although the accompanying history DVD only covered Powerslave and Live After Death, the tour was clearly designed to highlight the entire mid-eighties period from Powerslave to SSOASS. The SIT Eddie was the one chosen for the branding, and SIT tracks were picked for the setlist... and that's where the imbalance comes in. There were four Powerslave songs, three SSOASS ones and only two from SIT. From my memory, I think this is what really started the legend of SIT being the forgotten classic album, and it really picked up when the Maiden England DVD and tour made things even worse. Granted, there were a few things people picked on before, such as there being no official live recording or the epic from the album not being played live, but I think before 2008 that was more trivia for the diehards than an influence on common fan opinion.
(The following is mostly speculation on my part with some opinion thrown in)
If you ask me, I can imagine Maiden having good reasons for not bringing out any of the deep cuts from that album. Most of the songs simply don't lend themselves for live performances. SIT is the album with the highest degree of studio magic, and Maiden always had the ambition of performing their songs live the way they were on the record. If it's true that they re-worked Heaven Can Wait into a live anthem, that may even mean they were aware of this as the album was being made and they felt they needed to compensate. If you listen to the bootlegs from the tour, songs like CSIT and Sea of Madness don't really spark. I'm not really sure why that is for CSIT, it's not all that different from Moonchild in terms of structure. Sea of Madness on the other hand has nothing for a crowd to work with. Loneliness was dropped almost immediately, and I can really see why, it must have been physically truly exhausting for Bruce to sing. Stranger in a Strange Land does slow the pace, although with the lengthy instrumental sections of modern Maiden songs, I don't think it would be as noticeable anymore. With Alexander, I can see a 50/50 chance of it picking up live, but the possibilities for crowd singalongs during the instrumentals are relatively limited and the most promising parts really end quite abruptly. I'm pretty sure Deja Vu would sink like a stone, there's nothing in there an audience could catch onto. That leaves us with Heaven Can Wait and Wasted Years, the only two songs that ended up being setlist mainstays, for good reasons.
I'm not saying I don't like SIT or the songs I talked about - I do! But I can see why Maiden don't pay so much attention to it in their setlists without them necessarily having to dislike the album. Maiden feed off audience participation and activity, so that's going to be their main influence over evaluating whether a song works well or not. Whether it's okay for us to just stand there and listen, I'm afraid, doesn't matter to them.