I aggree, the new system is not only way less efficient, it also feels really out of place compared to the old one, for the reasons you mentioned.
I understand that the old system is a mess of code and i cant really comprehend how hard that must be on the devs, but it worked flawlessly for me and i really loved it. So i have to disagree with them if they feel this new system is more like what they envisioned for the game because it ruined our experience with the beta which was very good up until we reached the point where we were able to start our fleet and have them take on this missions.
I hope they find some middle ground because otherwise this beta has great potential.