Help in the design of a super low power device
OK, here goes...

In terms of safety, you will want to have some sort of protection against overcurrent faults at the power input stage. This could be a fuse, PTC resettable fuse, dedicated power management IC or a custom analog solution - but for this I would look at a PTC resettable fuse vs a traditional wire fuse. PTC should be cheaper (assuming you fit a holder for the wire fuse) but the wire fuse will likely have a lower resistance, increasing efficiency.

Additionally, since the motor power source is likely to be an even more powerful (and hence potentially dangerous power source) you will want similar current protection here - likely a traditional fuse as close to the power source as possible. This should be rated to protect the cable from exceeding its maximum allowable current.

Since you are controlling a motor, you need to consider the impact of the system failing with the motor on. Is that dangerous? If so, you will need to implement radio packet checksumming on the microcontroller to ensure that you don't respond to accidental interference from other sources. You should also really have a "keep-alive" signal coming from the control radio which you monitor using a hardware watchdog - if you don't receive a "keep-alive" every X seconds, the hardware watchdog kicks in and cuts out the motor.

Additionally, you need to consider the environment that the product will sit in and ensure that you encase it appropriately to protect from humidity, water ingress, dust ingress etc.

You have already hinted at EMC certification - you will have to go through this for both your unit and the transmitter that we can't see in your diagram. You will also have to go through the relevant product certification for your area regarding the type of device this is classed as. For both of these you will be needing consultancy from a firm specialising in compliance engineering, as this is clearly not your area of expertise.

As far as the battery voltage regulation goes, a switched-mode DC-DC converter will bring higher efficiency (if properly designed) than a linear regulator for all but the tiniest of  power draws. For low cost, you should be looking at an inductorless step-down charge pump for this.

Regarding battery charging - if you are able to charge the battery, surely it is better to use the available power to run your unit and forget the battery altogether? Unless you are designing this for an area with unreliable or intermittent power.

The schematic below allows for powering from a Lithium polymer cell with minimal loss (no diode drop) along with automatic disconnect should a charging source become available and charging of the cell itself. The charge pump follows after, and unlike some comments have described, can indeed reduce voltage! Although it will be about as efficient as a linear regulator for the 1mA periods of operation, it will be more efficient when larger bursts of current are required.







simulate this circuit &ndash; Schematic created using CircuitLab

To be honest, if you want to turn this into a product you are going to want to find an electronic engineer with experience of getting stuff to market to take on the design for manufacture and handle certification. But my answer should at least give you the gist of what you are looking for.