A lot of that "crap", including many of the hoses on the intake manifold, is for VTCS control.
From
www.mazda-speed.com (you should do some searches on this site for VTCS deletes):
VTCS is a tumble control system that effectively emulates varied valve lift by decreasing the volume of the intake channel. This gives higher intake velocities at low RPM, causing the air to "tumble" in the combustion chamber, making the fuel and air mix better improving emissions, and possibly giving a little better low RPM torque if implemented correctly.
The Adaptronic ECU can control VTCS but many guys simply get rid of it.
If you remove VTCS you can get rid of all that "crap" - I did this when I switched to the squaretop/flattop intake manifold. The OEM intake manifold has a lot of extra barbs to support VTCS which you'll need to block off, in addition to disabling the VTCS butterfy valves - the squaretop doesn't have VTCS or these extra barbs so looks much neater (and more legit).