Currently, advance circuit logic is usually a huge mess of spagetti made by combinators, deciders, and wires. Really ugly and space consuming. It would be nice if there is a small building that I can throw all those mess in.

This building should be small on the map, maybe 2x2 or 3x3? Smaller inside area than the mk1 factory, no input/output window, but support signal wires.
And it would be awesome if the graphic fits the style of the logic combinators.

I've heard this suggestion a lot, and I do like it, however Factorissimo's scripted circuit connections are pure poison for UPS if you begin using them in the manner you describe here, because reading and writing circuit signals through the Lua scripting engine is painfully slow. I've discussed this with the Factorio devs, and we don't see much room for improvement there and have settled on blaming Lua for the fact that you can't make circuit connections more performant.