The only reason I thought Store Spell was too powerful was because it's way better than anything you can do with a normal familiar. Even the few players I've known that made an attempt at actually using thier familiars, (in one recent game, the wizard had had an owl familiar thru six levels of play before he finally used it to do something- a scouting mission) and thus made them a useful addition to the party, would drop them in a second for some free extra spells. Yes, they'd have to Store them beforehand in downtime, but that's not much of a limitation. There would have to be some kind of cost or it would just be a freely used spell battery. By making it work like Scribe Spell, but at a discount, then at least there's some kind of limitation.
I could see the Store Spell ability working ok if there was some kind of, at least temporary, risk or cost associated with it. Just something so that using and "recharging" the spells doesn't become a completely safe, standard practice. Otherwise it's like having a "free" magic item- in this case, a bundle of scrolls you can refresh at will. (It'd be like having an animal familiar that coughed up some low level scrolls every morning. Who wouldn't want a familiar like that compared to a regular one!) And it might be a minor boost in power at the levels you get them but any spell can be useful if your creative enough, and who couldn't find a use for a few extra magic missile spells.