Good stuff, Tachyon! I notice you replicated a few of my ideas, but you have some great ones too. Lovin' it! Here are some more of mine:
This one is very simple - its just a Beam Saber built into the MS's forearm.
A Psychommu jamming system. I guess it would come down to the strength of the Newtype pilot; the pilot's MS would be equipped to broadcast his Psycho Waves as interference, which would block an weaker Newtype pilot's Psychommu control signals to Funnels and Bits.
I have always wondered why starships in the Gundam universe don't have I-Fields. Or, for that matter, Psychommu or Quasi-Psychommu systems. And thus Bits and Funnels, etc.
Considering that extremely powerful Newtypes (like Judo and Hamaan in ZZ) could actually power their MSs with Newtype energy alone, Id love to see a new kind of MS powerplant -- one which allows the MS to run purely on the pilot's Psycho-energies. Another option would be a Psycho-Battery, which stores the pilot's Psycho-Energy as extra reserves of power. Come to think of it, this could even lead to a kind of "Psycho Leech/Vampire" system in which an MS or MA can actually suck away the Psycho-Energies of other Newtypes in the area, making them weaker and itself more powerful all at the same time. In a Gundam UC0401 game I played in, the ref even had a giant Psychommu MA which used smaller Pyschommu MAs piloted by cloned Newtype girls as one-shot, disposable energy cartridges for its massive beam cannon!
This needs a better name, but the idea would be Psychommu Radar -- a sensor system which amplifies the Newtype pilot's ESP ability, allowing him to detect other people at very very long distances (and perhaps even intuit enough about their thoughts to identify if they're in a ship or an MS or what). At long ranges, ships and MSs and rocks and such would still be undetectable, but human minds would be quite clear.
In Seed, there are N-Jammer Cancellers. They are quickly outlawed, but they do exist. I could see the Gundam universe developing Minovsky Jammers, which could do such things as turn off I-Fields, Minovsky-Drives, Minovsky Craft Systems, and even destabilize Minovsky Compact Fusion Reactors (causing enemy MSs to just explode!). With this kind of system around, alternate power sources (like SEED's battery-powered MSs) and the above-mentioned Psycho-Power Systems would be very useful indeed.