The issues that I dislike are:

1. The fee on the days where I am not crossing a toll facility.
2. Charging me the full cash price of the toll when there is a discount for pass-holders.
3. The inability to disable LPR-based systems when the toll facility has a dedicated cash lane. (This occurs in Chicago where most albeit not all toll plazas have a cash option, perhaps in some cases exact change only).

Depending on the metropolitan area, simply avoiding the toll facilities may not be a viable option. I've paid the $2.95 upcharge on National's program before, but while they claim the right to charge me for the remaining days of my rental, they never have.

If there are any members of the business travel media watching this thread, I'd be really interested in finding out what California agencies' policies are about reimbursing employees and contractors required to follow CA travel policies when the driver crosses a facility with PlatePass only once during a multi-day business rental. I suspect that most agencies' policies are to only reimburse for the amount of the toll and the amount of the rental, and since PlatePass fees are not included in the rental, the driver is out of luck in terms of gaining reimbursement.