Yurch,
Well put... The ion is the only weapon that doesn't "feel" right in this game - to the point where I've stopped using it, even though I know it's quite effective.
As a matter of fact, long, long ago I worked in a physics lab that did experimental ion beam research. (Just a warning though: I'm a little rusty, because this didn't end up being my field of expertise!).
But, just to convey some sense of how hard this is to do: We had a very high voltage (> 10,000 V) power system the size of a truck, hooked to a cathode in a small vacuum chamber. Ions would shoot out of the cathode and strike the target, which was only a few inches away - inside this high vacuum chamber. The result was about one Amp of current into the target.
Air molecules certainly dissipate an ion beam's energy (hence the vacuum chamber in the lab).
So game-wise, it would make sense to have a big penalty for shooting one of these things through an atmosphere. The energy delivered to the target should be some strong function of 1) density, and 2) range. This could be interesting, because the ion beam could be a nice standoff weapon on an airless moon, but would only be a short-range "dogfighting" weapon on the green map, say.
Also, if we wanted to include some "physically-inspired" ion weapon drawbacks:
1) Size and weight
2) A chance of EMP'ing some teammates in your vicinity, due to rapid discharge of capacitors. 3) A long recharge rate, b/c capacitors can only charge so fast.
4) The ion weapon might not receive damage well... Envision a violent shower of sparks and EMP side-effects.