Stay with the airplane
I did have a squadron mate who was leading a flight in the break and accidentally switched off guard on his radio in the turn downwind. Unfortunately for him, his radios were also on the wrong frequencies, and he missed the fireworks display set off by tower at the approach end of the runway. He landed gear up and he told me later that it was a bit noisy, but the aircraft slid to a stop. "It was a sickening feeling," he said, "when you know you should be touching down but are instead sinking through ground effect." He knew something was up, just couldn't figure out what. So landing with both gear up doesn't sound too bad to me, and better than an ejection. I would be interested to know if anyone has heard of taking the gear at the end of the runway in such a case?
I have known a pilot who took an ejection over the ocean after a mid-air in an ACM (dog fighting) engagement. He was flying within a week, and, although the accident investigation found him accountable, he remained in the Navy as a pilot. I don't know if it precluded him from being selected for CMDR. It certainly could not have helped.
At sea you try to get aboard the ship and stay out of your chute, especially true if it is dark out. Even a controlled ejection at sea is risky. Instantaneous G's in the A7E ejection were 40, which is enough to make you lose consciousness during that phase. There is a burnout phase of 20 G's. It is a 0-0 capable ejection seat, which means it will give you a swing or two in the chute if you eject at 0 altitude and 0 airspeed. Generally speaking, the envelope of the seat, or when can you can safely eject given your descent rate versus airspeed, is complicated and I don't remember having any quick way of knowing when it was safe to eject. There were points on the envelope that we memorized. For example, an ejection over 400 knots can dislocate legs and arms, not necessarily in that order. Most of the accident investigations I read, where an uncontrolled ejection was attempted, the pilot initiated outside the safe envelope of the seat. Pilot's like to stay with their aircraft.
Each emergency is evaluated by the pilot, and then, if time permits, maintenance and the skipper, after which a course of action is determined. All of these things factor in to a decision to stay or eject.
Over water your troubles are just beginning when you are in the chute. Once you gain consciousness you have to prepare for water entry. There is a possibility that you can get entangled with the shroud lines. The parachute also is a great sea anchor, and will drag you under. The procedure was to release your Koch fittings when the raft hit the water. The single person raft held your survival gear and was deployed from beneath your seat. It was on a 14 foot tether. To give you an idea of some of the risks you might not consider. My squadron mate hit the water, which was at around 60 degrees Fahrenheit, he was in a wet suit and wearing his Nomex flight gloves. By the time he got to the raft and tried to haul himself in, his hands were numb and useless. He had considerable difficulty just getting into the raft, let alone then using the emergency radio to coordinate with the rescue aircraft and helicopters.
By the way, the other plane in the mid-air lost the section of wing from the joint outward (basically the whole wing), where the aileron was located. Three redundant hydraulic systems maintained the hydraulic flight control system. He stayed with the aircraft and eventually was diverted to Crete where he did an emergency landing. Again, it is worth pointing out that there was no ejection even in this case. There was also plenty of time to talk with maintenance, test the flight characteristics of the aircraft near gear down speed, evaluate the situation, and decide the safest course of action.
The point is, as a pilot I always wanted to stay with the aircraft as long as I could. In fact, the only "standing" controlled ejection procedure I heard discussed was the case where you run out of fuel at the ship. They steer you to some location, where the rescue has been coordinated and you eject.
Use the net
With a missing strut or wheel the standard procedure on the ship is to take the barricade. I was covering the last recovery as a hot tanker. I was in my A7E with a buddy store and 2,000 pounds of gas to give away. The designated tanker was an A6 circling at 5,000 feet, I was turning and parked right on the foul line near the Island. If the airborne tanker went down for some reason, and couldn't fulfill its mission as tanker, I would replace it taking quick cat shot off the bow.
I was up departure on one radio, and listening to approach on the other. The last aircraft coming aboard was AJ501, an A6. I heard the pilot's initial call of "Alpha Juliet 5-0-1, ball." The LSO had a welcoming tone to his voice when he calmly responded, "Roger ball, a bit left for line up." I was sitting on the foul line and watching the approach. I heard the LSO's call for lineup, but watched the A6 drop its right wing, which was pretty closely followed by another less welcoming call for "Left for line up!" from the LSO. The driver of the A6 dropped his right wing again and was now in close.
I just sat there as he boresighted me on the foul line. Didn't reach for my ejection handle between my legs, just watched with my eyes wide open. Incredulous of what was happening. It never got past my eyes into the working part of my brain. The LSO sounded downright rude on his last call with "LEFT FOR LINEUP! WAVE OFF! WAVE OFF!" Even today I shiver at the call. The pilot reached enlightenment at that point, with me a close second, as he dropped the left wing hard with the ball going off the top of the mirror. There were probably some power calls in there as well, I don't remember. It was a very big correction to centerline with military power coming back on the jet, and the A6 impacted the deck on its left strut, which subsequently snapped off and skipped, sparking its way down the deck with a high final arc to its trajectory as it disappeared into the night sea. Power was at military and the aircraft boltered.
I don't remember if they went and got some gas, but the pilot had time to collect himself because they had to prepare the barricade. There is a good scene in the movie Top Gun where an A7E takes the barricade, and shows the crew raising the pylons. The barricade is basically a big net strung between pylons that are raised up out of the deck on either side of the landing area. The critical point for the pilot is that the top of the barricade, that suspends the net, is a wire cable that is capable of cutting the airframe in two if the net is missed on a high approach.
The aircraft returned, for probably the pilot's most difficult approach of his career. The LSO will make the approach window smaller due to the risks involved, meaning that the aircraft will be held to smaller differences from speed and glide path and waved off earlier in the approach. It was a perfect barricade landing.