I would probably always choose the trip that allowed for more time in Antarctica!
I've done a cruise each on the Explorer and the Orion, the Orion was the ship I was on for Antarctica. Aside from the size, the main differences would be that the Explorer has a mud room where you can keep your waterproofs and boots. On the Orion everyone left their boots in the hall outside their room, and the waterproofs draped over the railing outside their room, which worked out fine. The Orion has a hot tub which was very nice after the polar plunge and I think a few of us used it sporadically. But it is outside and so very cold getting in and out of the hot tub.
The Explorer is slightly larger, but still small enough it is easy to meet people.
In general, when cruising I always try to get rooms on the lowest deck and near the middle as there isn't as much motion in that part of the ship, but I don't remember it being rough except when crossing Drake's Passage. And probably no difference between port and starboard. I've never spent much time looking out the window in my room anyways.