For larger DIY/hobby projects using 32-bit processors there are now many hardware options and the future will bring many more. It would be a shame to be limited to choices made by the Arduino company.
About 30 years ago big science faced a similar situation. From the late 1960s to mid 1980s DEC (Digital Equipment Corp) minicomputers dominates control and data acquisition in large science experiments. DEC supplied the software environment with systems like RSX/M, a real time system, and VMS for larger VAX machines.
Around 1985 single board computers based on the MC68000 and other microprocessors started to be used There was no standard OS for these boards.
Fortunately two of my friends, Jerry Fiddler, and David Wilner, had left the Lab in 1982 and founded Wind River Systems. Wind River developed VxWorks which is a flexible RTOS that can be targeted to a wide variety of processors. VxWorks became very popular in large physics experiments, space experiments like the NASA Clementine moon probe, and the Mars landers. This defacto standardization was really important for big science at that time.
UNIX on SUN and other work stations became the standard OS for operator consoles and other non-real time applications . Linux is now the best choice for boards like Rpi and BB that have Cortex Application processors.
The problem is that there are too many RTOS choices for micro-controllers like Cortex M and PIC32. Many companies are supporting FreeRTOS but it is not technically outstanding.
I like ChibiOS/RT but it only has great HAL support for STM32.
I think Arduino is like Digital Equipment Corp and will fade in the same way. There will are too many other outstanding hardware options and there will be even more in the future.
There is not an obvious software solution for DIY/hobby users. FreeRTOS supports a wide variety of hardware, just look at this list http://www.freertos.org/RTOS_ports.html. FreeRTOS is just not very exciting.
Too bad it is so easy to build a little RTOS kernel, this means there are many half baked RTOS systems instead of a project like UNIX and it's follow on, Linux.
westfw is right, the problem is the proper OS for DIY/hobby users.
Or an OS for Teensy/NXP/ST/TI that is better than the current bare metal, without sacrificing the "ease of use" of the Arduino libraries. But I don't think that either one exists yet.