I like the new system more than the old one too. But...
I still see a problem with grandfathering such secondaries as low heat generation e.g. G1 rail guns and PAs with -50% heat generation - there is no indication of what happens to such modules in the new system if it is stays as it was shown then we have a problem.
FD is trying to make us more attached to our ships, but it is too late with all the ship storage etc.. The new system makes a step towards "sense of pride and accomplishment" for your upgrades - you just roll once choose experimental effect and then pin the blueprint and play the game and kinda shape your ship to perfection of your liking - it grows with you, you get attached, you value every step on that journey. The problem is that we (most of us, as players) have already lost that sense because we own a lot of different ships they are no longer our extensions they are just different tools that we change as we see fit and when we want. Thus people complain that they won't be able to upgrade their "fleets".
I think you're being disingenuous. Whether you have one ship or 100, the core experience of the game is and always has been the swapping of modules and experimentation with loadouts to pursue different activities in the game. One ship cannot do everything, not all at once anyway. Which means continual tinkering with builds, exchanges of modules, upgrades, etc.
People maintain "fleets" because no single ship can do everything, no single configuration can do everything, and reconfiguring your ship can take longer than building a new one from scratch and the next swapping between them on an as-needed basis.
The new update ironically does more to encourage this kind of ever-expanding fleet business, because it locks you in to whatever configuration you come up with, and severely penalizes you for changing it.