Several issues, which I have, most unfourtunatly, not had the time to write up over the last few days.
The most obvious is, over course, the ultrasound system that you insist on keeping here. If you really want this ship approved, you should just drop the damn thing.
M'kay, the thing is that the bone (as stated in the links you guys have provided) of the skull absorbs energy of the ultrasound and would simply block a signal of too low a amplitude. Since this was noted, and has been, a concern and problem with current ultrasound energies and amplitudes, it means that the amplitudes needed to "saftley" probe proteins on the picoscale would be below the lower limit by many magnitudes. Further, since the power of a sound wave increases by the square of the frequency (according to the equation P=ξ^2*f^2*c*ρ/4π^2; which would be on the order of 1e15-1e18 fold increase in power) the total energy delivered will be increased massively as the frequency rises to the needed levels (and since the amplitude must stop decreasing at a much, much smaller number than the frequency).
Since this system is intended to operate as a M-M interface it must be introducing and gathering information and data to and from the brain ata extremely high frequency (as in ops/second, not the sounds frequency) so its off-time will be very small, and no where near what would be needed to maintain safe operation power levels.
=Creation engine:
I do not see the need for this device. It does much of what the nodal system already does, and throws in a few more precedents just for the heck of it. But beyond that, why would you want to centralize this system so? It makes it so that the entire ship can be utterly devastated by a single good shot with a starship-grade neutron beam.
=Stealth:
You can't do that Uso, heat is the most useless form of energy, it is entropy. You can not eliminate it or change it wholly into usable work, there will always be waste energy, and given the amount of energy involved with a starship and incident radiation, this will be quite large. (and Jatsu, hyperspace sensors exist, so just venting heat there won't get you out of trouble with the stealth)
Yet again you use a double standard. You love to use the justification that, since the SARPP has a much higher level of technology than now it should have incredibly better sensors, systems, etc and that makes whatever you are pushing A OK. If I apply that here, even if you can reduce the waste heat to a tiny, tiny fraction of a percent of the ships total energy use it should glow like a small star on any SARP level sensor system, never mind if they are using multiple sensors to scan space.
=Heisenberg Compensator:
This thing needs to go; there is not a chance hell I am going to let this go cannon or let you sneak it in and set another tech precedent. It is entirely wrong on every level.
=Weapons:
Remove that "OMGâ€