Firstly I'm sorry you feel let down by this change in direction. We provided free accounting software for 5 years but I'm afraid we were unable to continue this arrangement, it was simply not possible to support users of all sizes for free, indefinitely.
I would however suggest that if you are managing 2 accounts, Affinity will be a more cost effective option and payment for this can be made on a month-to-month basis, rather than an annual commitment.
Also just to clarify, the account size is based on all nominal ledger entries, not just invoices, so if you have a lot of bank entries this will also push up the total count. You can view a backing report for the account size in Account Settings >> Company Settings.
EDIT:
Also can you clarify what sort of customisation are you looking for? A Power User subscription would actually give you a great deal more options in terms of customisation.