FACS calibur can analyze 3 flurochrome channels- FITC, PE and PerCP. If upgraded a fourth flurochrome APC can also be analysed ( read about the time delay calibration when a laser for APC detection is added). FACS Aria can analyze upto 9 colours, I guess. So in aria one can use many flurochromes. This is helpful esp. when one is looking for a sub population in a sample. In such a case, one can add lot many markers with different flurochromes, and study a population present in very low frequency.
So if you have a sample which needs to be analysed for upto 4 markers use Calibur. The machine is really something. Very easy to use and analyse. If you want more colours, want to acquire lot of cells with high flow rate or sort them, use Aria.