That's the beauty of an ongoing development. I have no doubt that feedback will bring slight tweaks to this system. I doubt they'll be massive, but I suspect they'll make the management a little more forgiving.
I do think that the system was built on the assumption that players would pin a couple of blueprints from different Engineers and work towards one of them (depending which proves fruitful), more one at a time than a load together. So in that sense, I feel you're probably at odds with how they expected the game to be played.
Doesn't mean that anyone is wrong - I suspect many do as you are doing. I imagine they're trying to find ways at keeping people from becoming Engineer powerful too quickly, at the same time they'll be wary that people don't get frustrated and walk. So yes, a middleground I suspect is yet to come.
I hope you're right my friend. I must admit though that I've been playing since before release and my faith has been waning somewhat. And don't get me wrong, There are great things about the update. I listed them in a positive feedback thread. I just don't think the aspect covered in this thread was done well at all. Here's hoping for a fix.