Just like any other SaaS, they are built for the masses and will never offer enough customization or too expensive. The only way to truly fill the gap is to roll your own. I suggest you find a developer that can truly deliver what you need and do it for a low cost, but make make sure they are available for the long-haul so that you can add features a few months down the road.

You will not find a $20 a month solution (unless you are a cookie cutter franchise business), but for less than $1000 you can have a stable, secure life-long tool with no monthly fees or privacy concerns.