I would highly suggest either having a the subversion repository on the same box as FishEye or at least a mirror of the repository on the same box. FishEye needs to make calls out to Subversion at indexing time for information so minimising the network calls will improve indexing speed significantly
One factor that greatly influences FishEye performance is where the repository indexes are stored. Make sure FishEye stores its data (the FISHEYE_INST dir if you have separate data dir) on a local disk, not on a network share or SAN. This will improve both indexing speeds and general performance.
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