Design for wire between server and access point and RF to endpoint device

We're about to design an inhouse industry network consisting basically of the following: 1 server connected via wire to up to 100 proprietary RF access points (basically embedded devices), which each can be connected via radio to up to 100 endpoint embedded devices. Something like this:

Now, I'm wondering about some design decisions that we need to take and I'm sure there are plenty of similar designs out there and lots of folks with experiences of them, both good and bad. Maybe you can chime in?

All endpoint devices are independent and will communicate their own unique data to the server, and the other way around. The server therefore needs to be able to target each endpoint device individually. Each endpoint device pairs itself with 1 access point and then talks a proprietary RF protocol to it, TCP/IP is not an option there.

The server will know which endpoint device is paired with which access point, so when the server needs to talk to an individual endpoint device, the communication must go through the paired access point. Hence, the server needs to directly address the access point.

Question: Considering the limited resources available in the proprietary access point, is TCP/IP between server and access point recommended for this scenario? Or would you suggest something entirely different?

I find the diagram confusing:

If this isn't its own network and the server to AP link is running on your internal company network, there isn't really an option, there must be a TCP/IP stack on the AP.

If this is its own isolated network then what is the router for?

If this is, in fact, its own isolated network then you are right, there really isn't a need for the Ethernet connectivity at all. The overhead you will see on the wireless is huge, your no overhead ideal data rate is 250kbit/sec, running ZigBee on 802.15.4 @ 2.4ghz point to point your real data throughout is usually around 20kbit/sec. A custom protocol should be able to obtain lower overhead but this would need to be defined.

If I were designing this I would choose a SoC for the AP that had on board 802.15.4 and CAN (Controller Area Network). Depending on size and data rate just get a PCI CAN card for the server and connect it up, use something like DeviceNet as your protocol layer for server to AP communications. This can be expanded by using CAN switches and repeaters. CAN is used all the time in industrial automation, a little googling can find you example of tens of thousands of nodes used in some manufacturing plants.