Having both options in just muddies down the game with unnecessary gunk.
It's not "unnecessary gunk" if it works differently and some players prefer it. Maybe Assembly Project isn't your cup of tea, but that's not a good enough reason to take it out of the game.
Is that not better? It seems at first glance that it would be. I must admit I find the old way terrible, and crippling, at least in the early game. If I want my planets to have any population at all, I have to not build anything, then I watch turn after turn tick by with horribly slow pop growth and no buildings. The Yor were one of my favorite race's in GCII but I barely play them now.
The biggest problem with fast assembly is that forces you build 5 at a time which means if you want to stay at or near your morale cap you have to do a lot of fiddling around to get the right populations on the right worlds. This is MUCH more micro than going through and taking Assembly Project out of your queues every once in a while.
As for building population on new worlds, fast assembly is slower than .7 assembly project, which had been buffed to 5x the speed of the beta 3 version, because it doesn't build any population until it is finished. That means if you have a new planet with say, 8 manufacturing, you will have to wait 13 turns until you see ANY growth.
Fast assembly is better for people who don't want much planet management. For players who only want to check in every once in a while, and don't mind that they aren't being totally as efficient as the could possibly be it is an easier tool to work with. But for players like me, who are trying to run the most effective empire possible, already have auto-upgrade turned off and most turns at least check in with each of my planets anyway, assembly project is a much better way to grow Yor.