I must say, assuming performance is acceptable, text file storage sounds ideal. Little chance of being stranded with a bunch of unreadable, outdated .gnucash (or whatever) files. I'd rather have a bunch of 100,000 line text files than a similar amount of opaque database files.
I'd guess the problem is not so much the storage format, but the interface onto it? If someone were to write an accountant-friendly front-end, would that take care of your file format concerns?
(of course this doesn't affect the other missing bits like invoicing, bank accounts, recurring transactions, etc..)