This isn't exactly related to the topic at hand, but ...
But if you did then the player could add 'bots or even aliens or humans or whatever, on new city maps and new mission maps.
I don't know about the new enemy types, exo types, or mission types, but it is certainly already possible to create a new city map and associated grid, and it may be possible to have both the user-created map and the default Port City map in the game at the same time.
If you wanted to create a new user-defined city map, then there are two ways you can approach doing this: way one is to find the current city map information and overwrite it with whatever you want your new city map to be; there is a possibility that this will not work if you change the city map image size (4096x2400, PNG format) or the number of grid nodes (125 nodes and about 135 connections).
Way two is to figure out how to insert your own city map into the game. This would require you to create a new city map image (the one included with the game is in PNG format with 4096x2400 pixels; I don't know if it has an alpha channel as I haven't looked into it) and a city grid map (the one included in the game is a list in XML format and contains 125 nodes and a number of connections between the nodes), and I suspect that you would need to go to C:\Program Files (x86)\Steam\SteamApps\common\Bionic_Dues\RuntimeData\Language\en and edit the file a_bionic.XML found within that folder to include the lines
<ln id="CityMapType_Name_PortCity">Your City Name</ln>
<ln id="CityMapType_Desc_PortCity">Your City Description</ln>
possibly with modifications to the tags (i.e. you may need to change the name of the city in the tag name, though I would hope not). The city map image and the city map grid node/connection listing are found in C:\Program Files (x86)\Steam\SteamApps\common\Bionic_Dues\RuntimeData\Images; the grid node/connection listing for the map provided by the game is PortCity.XML, while the map image is PortCity.PNG.
Grid node coordinates appear to be pixel coordinates in PortCity.PNG, with the horizontal coordinate listed first. My assumption would be that grid coordinates start at 0,0 in the upper left hand corner of the map image, with positive down and to the right, though I may be mistaken on this. I do not know whether or not the game requires the map image to be the same size as PortCity.PNG is, but if it does, that image is 4096x2400 pixels, nor do I know if the game requires an alpha channel for the city map. Grid node connections appear to be point to point and bidirectional (i.e. you do not need to list node 18 as being connected to node 17 if node 17 is listed as being connected to node 18, which suggests that a good way of creating your node connection list is to do so in order until you run out of nodes with connections to nodes whose node number is greater than their own).
I was unable to find references to Port City, PortCity, Port, or City (case insensitive) in any files other than the ones I have listed above, though that does not necessarily mean that there are no additional locations which would require modification before you would be able to add your own city maps into the game. I expect that Way 1 would work, at least as long as the total number of grid nodes and connections and the image size were unchanged (it may work even if the total number of grid nodes and connections, and the image size, were changed, so long as the game does not check to ensure that these files match a certain set of parameters based on their default condition); Way 2 would be the better way to do things if it does work, but might not depending on what the game expects to see for a city map to work.