The primary limitation on ion drives is the power available to the spacecraft itself.  There are secondary issues with respect to neutralization (you don't want to charge the spacecraft with respect to the background space plasma) and erosion of the grids used to accelerate the ion beam itself.  I'm not completely sure why erosion is such an issue but it tends to be something which limits the lifetime of the drive itself.  The power limitation is the more critical one as solar cells produce a strictly limited power output.  To get a high performance ion drive requires the use of a nuclear power plant according to a soviet expert who gave a talk on this years back at an ion source conference.

I had an argument with the person behind attack vector: tactical about their use of fusion drives simply because I can't for the life of me understand why given the option someone would not use a fusion reactor to produce the power to run an ion drive rather than farting around using fusion exhaust particles to drive the ship.  Based on my work I can't see why making large scale 100-1000 A, a few MeV energy Xe+ beams would be a difficult task, that would require only several 10s of MW of power in the worst case.  And the thrust available would be easily in the 1-2 G range which you could always add in extra combat thrusters to enhance by additional plasma drives.  And at 1 G it is only a few days from earth to Jupiter even including turn around.  Even at 0.1 G it isn't an overwhelming length of time (comparable to early sailing times for cross atlantic journeys).

However, so long as the power supply is limited to that possible by solar panels ion drives will stay limited to low thrust tasks.