Overall, I'm actually pretty excited to try out some new builds I made in beta, and the system is going to give me far more upgrades than downgrades.
It's also a bit easier to plan ship builds, since the end results will be the same. It's also easier to consider what you could go up against with an opponent (not that I do PvP, but I found myself correcting my heat efficient FDL build, when I realized that with clean drives, anyone else in an FDL with dirty drives would make escape impossible).
But there are some things I still wish FD did to keep engineering variety in the game.
Currently there are modifications that don't really have any variation, either because one of the secondary effects is vastly better than the other choices, or you are after a particular experimental for a weapon. For example, the G5 FSD secondary "Mass manager" is mandatory if you care about a greater jump range on your FSD, basically reducing your choices to one. I would of much prefered if they integrated this into the base roll so that the other secondary effects were more worthy of consideration.
I've pretty much been playing the same tune for a while, but I think multiple secondary effects should be possible for each module, preferably as some form of reward after leveling up an engineering tier to keep the player invested in the entire engineering process from start to finish.