Many folks have huge trouble with building extra packages for the cRIOs (that are either missing or outdated), not to mention reproducible deployment and configuration management.
In industrial environments, we need a very high degree of customizability and reproducability, which the current nilrt distro just cannot provide. Setting up such an environment from scratch is a huge work for users, which usually aren't Linux embedded expert.
Therefore I'd suggest an fully automatized deployment of development environments, which are also easily customizable for the user. Major keypoints are:
a) development environment setup:
* container-based solution that can put together an environment automatically, using well-proven standard technology (eg. docker, ansible, ...)
* executable documentation: use declarative approaches, that are easy to understand and allow automatic documentation (eg. for verification / validation)
* use a recent, well-maintained standard distro (inside the container), and use off-the-shelf standard tools where possible
* fully tracable source control via git
* easily customizable: the user can fork off his own configuration from the appropriate upstream release, customize to his needs and later rebase to newer upstream releases if wanted
* automatic setup of package mirrors, binary repositories, product specific local deployment and HIL environments, etc.
b) target build environment:
* highly reproducable - even after very long time (eg. also allows automatic source code mirrors, etc)
* executable documentation - the configuration can be easily understood and used for generating documentation
* based on a Linux embedded experts community
* supports building for several (including customer-specific) target platforms
* supports easy configuration / customization of installed packages, as well as features selection and tuning of individual packages
* supports easily adding own software
* supports maintaining customized system configuration with image building
* fully tracable source control via git
--> the natural choice is using PTXDist (fast, reliable, reproducable, excellent expert community)
I'd estimate about 6 man-month (for a lone developer) for the initial stable release of the core system, plus another 6 mm for additional tasks like user documentation, examples, target specific configurations, etc.
Costs: about 200k $ (including extra buffer)
Equals sales price of about 25..30 avg. cRIO units. (RIO break even likely at about 50 units).
OR 
