All lines do not need be to the same although you will have higher energy efficiency (more flow rate) with larger lines. If you are going to use different size lines, then use the larger ones on the suction side because you always want to keep suction head much less than return head to avoid air leakage and cavitation problems. I would recommend 2" as a minimum and 2.5" if want the system to be a little more efficient (~4%). Use separate suction lines to the equipment pad from each main drain pair, if you have one, and from each skimmer, if you have more than one.
Also, the size of the skimmer ports is not really that important since you can always use an adapter to step up to a larger pipe size. They also make skimmers with larger ports if you haven't purchased them yet.