Oh that's probably right. Maybe the fact that engineers/researchers are deployed in the base defense had me confused. Well, if they are deployed they should have all Personnel stats even if they are sub par. That way even if your all your soldiers are away or died defending the base, you'd still have a chance to win. Let's say your last base defending soldier is KIA and you're left with a crew of engineers. You'd want to defend the base with them and be able to equip them even if most would die, being weak soldiers.
I have at least one idea for more involvement on the R&D side (inspired by another post here): juniors, seniors and chief. What could that bring to the gameplay? Well, it could be several things! Imagine leadership affects research/manufacture time. Starting out with maybe only a bunch of juniors, no leadership boost is present in the scientist teams. When a senior is recruited (or achieved through experience) it will grant a speed boost to research/manufacture. An even higher bonus could be granted to chief (and like the Commander rank, there can be only one Chief Scientist/Chief Engineer). Other aspects could be that you need a senior/chief to be able to take on a certain task. Or like the other post said (about scripting) there could be a level where you need to bring back your Chief Scientist that was captured/abducted/taken hostage.
I'm sure this would make the R&D aspect of the game richer, but like with other ideas it's a lot of work and perhaps a lot of change to the gameplay.