Well, another idea thrown into the arena:
In JA2 you hire repairmen and doctors just like any soldier, with name, picture, combat stats.
As Chris wants to change how the base works, why not make "science" and "manufacture" both a stat (how good is an employee?) and an occupation. Thus the faceless scientists/engineers become persons. If done like in JA2, the player would hire x employees, select them from the list, put some of them in the Chinook, some in the lab and some do manufacturing. Of course the science/manufacturing stats go up used.
Advantages: As mentioned, all employees become someone the player can relate to.
Also, it allows more flexibility in the gameplay: Do I replace the wounded guy with a scientist - bad combat stats and risking a scientist - or do I hire a new soldier - costing money. Do I need more science right now, or more MiGs?
To be honest, I like the XCOM1993 approach to scientists a bit better than above idea, but as Chris wants to change it it would still be better than dumbing down to the EU2012 level.