Hi Anthony,
These are all great points, and areas we hope to have covered if they are not already covered by some solutions.
The issue is that we are a new entry into the POS world, its hard - if not impossible - to create a great product that also does everything . . . I think back to 1984 and two major PC manufacturers.
In the end a beautiful design and simple interface won that round. Shopify POS is an ideal link for an ecommerce retailer that is starting to add in person sales. Shopify POS is not a full featured POS system. We don't have every feature that exists by design.
For inventory and management this is already handled in Shopify via external apps for more complex needs. There are apps such as this one https://apps.shopify.com/rmsify which can make the link.
Employee management can be handled via many third party tools as well, often free. We could have added this in - but again, we would add complexity, time and cost to the product. We are actively monitoring customer interest in these areas as we want to be the complete solution for customers that POS suits. For example employees can clock in on their smart phones or online using http://www.shiftplanning.com/
Our issue with combining with the hardware device is partnership with the banks. To support more than one system we would require multiple agreements. We are amenable to making the system open but its difficult to achieve security across more than one banks system.
We have great security architecture for online integration with many gateways, and with our POS reader to Shopify Payments, but its a bit of a technical challenge to not use external terminals to make the link. The double entry issues exist with cash register terminals also, so its not a new retail issue.
The exchanges are currently possible with the store credit, and back to the credit card as a refund but it does not currently track the balance of exchanges.
We're excited to keep adding in features that will benefit our merchants and really appreciate hearing how you find the Shopify POS experience.