I've found some SoC's:
JN516x needs BeyondStudio IDE, which is available only on Windows.
JN517x seems to be developed not for mass market since no online shops sell them.
BTW, these MCUs were originally developed by Jennic and has 32-bit RISC architecture.
KW21Z (KW41Z) has Cortex M0+ core, and needs less current. IDE is crossplatform eclipse-based MCUXpresso.
And I know that Xiaomi uses JN5169 in theis sensors and hub, as long as Aqara, but not KW21Z.
Which MCU is the best to start development?
As you said already, JN5169 is more mature, but not with ARM Cortex M core. This may affect you for your toolchain, SW development environment.
KW21/41 is with M0+ and MCUXpresso IDE which has a version under linux.
Note that KW41 has both BLE + Zigbee/802.15.4. If you need a zigbee gateway design, it might be helpful.
Alternatively there is a JN5189 on the way. The chip can be searched on nxp.com. But I don't see yet datesheet, tech doc etc. Don't know when they will release them. JN5189 is with the Cortex M series core.
So at the end it is up to you to choose the part based on the project. The power consumption / price etc. are also important factors if you are making big volumes.
Which MCU is the best to start the development?
It depends on your final application.
For the JN and the KW we provide Zigbee Sensor examples. However, there is not support with Linux working on the JN.
The MCUxpresso is supported by Linux. Could you please provide more details about your final application?