CM (particularly CM 9-10.1) have much larger system partitions than GB ROMs, but they also have larger data partitions as well. When ever I come across having low space, I just go through my apps and uninstall the ones I haven't used in a while.
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Yeah I think cm might be larger than stock roms, or the data partition is made smaller so leaves less room for apps. Back in the day there was a patch on the HTC Hero that let you configure partition sizes for cm7 so you could whittle the system partition to bare minimum and make the data partition larger. Haven't seen anything like that for our epics though.
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