This is purely speculation, but I feel like Tsunku might've just been stuck on this single and couldn't think of more than one new song. Maybe he just didn't have any inspiration for a second a-side, so he went with re-arranging Kanashiki Heaven.
I personally think my issue with it is that it's an a-side. If it'd been a c/w, or perhaps part of a triple a-side, I might've been less bothered, but as it happens, I don't like the song and I've always been bothered by re-releases as main tracks on singles (Chokkan 2, etc). Covers of other artists' songs are different than that, imo, and don't really count.
(I'm also slightly annoyed because I know Maimai won't get any lines or anything, and there's too much Chisato for my liking, but eh. More for people who enjoy it, I guess.)
Otaku, i think we only get 2 songs because of the double A side thing.
But initially, we got c/ws with the double a-sides. One・Two・Three, Brainstorming, Wagamama Ki no Mama Ai no Joke, Asian Celebration, Motto Zutto Issho ni Itakatta, Kanashiki Amefuri and Tokai no Hitorigurashi all had c/ws despite being double a-sides. Sure, S/mileage and J=J haven't had c/ws with theirs, but the other three groups have. So I really don't think that's the issue, imo.