What you need to consider is the actual area of each pipe. For example a 1" pipe has an area of 0.78", where a 2" pipe has an area of 3.14". You don't have to automatically double the pipe size to get double the capacity, but it doesn't hurt anything to go too large. Also keep in mind that a single 4" pipe carries a MUCH larger volume than two 2" pipes.
What flow rate are you planning on using through your filter? Under pressure, you can push 3600gph through your 1.25" pipe, but once it loses pressure inside the filter, the water will not flow back out the outlet pipes at the same rate. If you want to push the full 3600gph through your filter (not recommended), then a 4" outlet pipe should work. If you cut the flow rate back to 2500gph or less, then a 3" outlet pipe would be fine.