First, the only issue of the Connect Card is half-fare disabled passengers still have to pay full price if they should want a pass. Offers passes at half fare, and to reduce fraud, redistribute half fare cards with photos.
Second, are passes. Offer a 7 day pass (7 days as opposed to a calendar week), a 14 day pass (since most get paid bi-weekly), and a 31 day pass. The prices can be fare x10, x20, and x40 respectively.
Third, the fare boxes are new. They should support register tapes which can be used for transfers. Keep e-transfers with Connect Card at 3 hours, and register tape transfers at 90 minutes. This will save on production of transfers that have to be made daily for every bus. To eliminate Continuation Transfers on the Funicular Inclines, it is simple. Connect Card - Free. Cash - $1.00. No transfers provided, but accepted.
Completely eliminate bus tickets, and paper passes. These are still being distributed, and likely through social service programs such as MATP, or Traveler's Aide. Instead, work with someone to build an API to allow these entities to have deposit access to a person's card by knowing their Card Number. The Connect Card system works, there is no need to be shy of embracing it completely.
As for ConnecTix, I personally find this as a pointless thing, but assuming it is to stay around, charge $1.00 for the ConnecTix card. Allegheny (or other supporting transit companies) should provide the Connect Card for free to residents, and charge $5.00 if it is lost. Cards no longer functioning should be replaced for free.
Last, allow a Family to have a single pool to work on multiple cards. I know families of 5 that are on a tight budget, so adding $25 to 5 cards is not realistic always. However, add $50 to a family account and allow the different Connect Cards to access those funds will be more viable to such circumstances.