We don't know if that is an issue specific to Isshin or something that's a general concern with bankai.
By that, what I mean is this: Aizen indicates that he was thinking of something specific to Isshin's bankai when he decided to slash Isshin. However, the theory on a more general level may apply to a lot of shinigami. Given what we've seen of bankai throughout the entire manga, there's always some kind of cost involved. Bankai cannot be used without consequences. Experienced, powerful shinigami may be able to minimise (or, more accurately, better control) the downsides of their bankai, but that doesn't stop downsides from existing, no matter what (ie, no matter how experienced/well-controlled the shinigami becomes, the downsides or 'costs' will always exist).
We've learned about 'costs' with several bankai (Soifon, Komamura, Byakuya), including some that have been implied to have 'costs' of some kind (Urahara, Kyouraku). Isshin joins an existing list, rather than standing out as unique for having some kind of problem with the idea of freely using bankai.
Soifon's once-per-three-days rules sounds fairly insurmountable. Had we been told it in advance of ever seeing her bankai, we might speculate that it's a rigid, unbreakable rule of her bankai. We still don't know how far she will ever be able to push it but the key message of her issue is that her bankai consumes a lot of reiatsu to use just once: whether or not she becomes better able to absorb such a high reiatsu output in the long run, the fact that it has a huge reiatsu cost probably isn't the aspect of her bankai that will ever change.
As a result, we don't know how insurmountable Isshin's bankai restriction is. Depending on English translation, Aizen's comment can sound like it's accommodating the possibility of Isshin being able to work with the restriction if absolutely necessary or it can sound like there's no negotiation on how unbreakable Aizen believes the restriction to be. Either way, however, it's Aizen's knowledge of Isshin's bankai that's being discussed, not the reality of Isshin's situation - and 20 years before Chapter 1 ever began, which means we don't know if Isshin's current situation is the same now, even if Aizen was absolutely accurate 20 years ago. Up until Karakura Town's battle, Soifon always thought she had to use her bankai once every three days: so was that what Aizen thought about her bankai, too? We don't know. The same could be true for Isshin as well.
Edited by Milareppa, 03 September 2014 - 11:36 AM.