Actually duck, I said the tears in the milky way were mostly minor. There are tears in other areas of the universe where the storms break through and wreak havoc (The Collective accidently crashed the two universes together in their attempts to end the war.) Its because The eye of the storm, so to speak, in the secondary universe are coordinates matching up with the milky way, thus the majority of storms are not in the milky way, save one or two 'freak' occurrences. Essentially its a sort of post apocalyptic situation... Set to return to normal in 500,000 years

Ion Storms could work, but it depends. It's likely to stop the regimental firing lines for cropping back up in every single battle, but if someone does want to do that (and there are situations where it might be a viable plan) then it sort of kicks them up the arse.