While designing their Fin/Swe, layout I guess Planet, when they saw that a Fin/Swe PC keyboard has eleven letters on two of its rows, just moved the two rightmost letters to the Fn layer and called it good, thinking "Well, Finns and Swedes are both used to have Ö next to L", which isn't incorrect, but perhaps not the best adaptation to a "no more than ten letters per row" layout. Unless sufficient noise can be made about it, I doubt they will change it, though. If they'd make an official keyboard remapping tool, they could start selling a selection of key caps to those wanting to customize. I'd gladly pay €10 for an Ä key cap.
What makes Ä so relatively common in Swedish, is probably the word "är", which means "is". According to that cryptography page, it's the sixth most common Swedish word, after i(I), och(and), en(a), av(of) and som(as). We find an Å in the eighth most common word på(on) while the first Ö is found in the twelfth most common word för(for). In the top thirty Swedish words, there are a few more with Å and Ä in them, but no Ö.
On a side note, han(he) is the sixteenth most common word, while hon(she) doesn't even make the top thirty. It seems we still are a fair bit away from gender equality...