Beast,
Are your parts in "families", or what kind of relationship do they have to each other? How many parts make one set to complete one order? How many times does the part have to be moved to complete machining?
The number of tools you will use to machine all these parts is an important consideration. Consider the toolchanger capacity. You would at minimum, need a dedicated toolholder for every tool you will use. Offline tool presetter would be important. Automatic loading of tool numbers and tool offsets for each program is also important for what you are trying to achieve.
Consider using fixtures on removeable pallets to quickly change setups. Expensive yes, but if the parts are difficult to set up, the time required to set up for one is a killer.
Pro E is pretty expensive, not? Take a look at OneCNC while you're shopping for software. You want something that most anyone can learn with a minimum of learning curve, in case your machinist quits on you.
First you get good, then you get fast. Then grouchiness sets in.
(Note: The opinions expressed in this post are my own and are not necessarily those of CNCzone and its management)