I still don't see this.
The new system adds more options, and forces us to choose between what we want a ship to do. The old system was not this great beautiful masterpiece of engineering, it was just arbitrary.
The difficulty in building should be in balancing what everything can do, not in the physical layout of the blocks. I see much more complexity and decision making in the new system than I do in the "just figure out how to cram it all in" previous system.
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Then put it in those terms without the name calling, please.
What you've said so far has basically been, from my point of view, "This is terrible because it makes us use X arbitrary shaped ship instead of Y arbitrary shaped ship". At the most, I see it as just promoting different shaped ships than before, while giving us more options in how to customize each ship.
The old system was arbitrary and counter-intuitive while offering no real decision making when it came to a ship. The new one isn't perfect, but its better than what we had. If you can come up with a better system, then by all means type it up and we can discuss it. I just really hate the whole "this solution doesn't fix 100% of everything, so it shouldn't be done" thing I see here and in the world as a whole. Incremental improvements are better than leaving things the way they are to me. This new system gives us lots of new options, while only removing gordian knot reactor lines. It simplifies the build process while complicating the design process, I see that as a good thing.