In an attempt to make this a shorter reply, I'm cutting out quotes. So in order to try to keep it clear I'm going to use the same numbers to respond to the same points.
1) It looks like its just coming down to you and I having different interpretations of the effectiveness of weapons at their extreme maximum range. Looking realistically at a bomber sitting at the extended flight ceiling, safe from ground defenses, his bombs now have a travel time of 8-16 seconds. That might not sound like much, but if you actually start a stop watch and let it run for twelve seconds, its immense. Anything that isn't permanently stationary, including AMSs and a vehicle being repaired by hand, is going to have ample time to escape. With no vehicle boarding animations, you can literally hop back in your vehicle and drive a few feet to safety with tons of time to spare. Any bomb dropped from that height is going to be fully visible on radar for the entire duration of its flight. While technically possible, a bomber at that height is sacrificing almost all of his effectiveness.
With that said, your targets as a high altitude bomber are limited to only things that cannot move, which includes CE and base turrets. Neither of those things grant player kills. CE is neither pivotal to a base defense nor is it hard to replace. As for base turrets, even in PS1 they're one of the first defenses to die and one of the last to get repaired.
2) You're not really imagining the same scenario as a bomber at max altitude. All a prowler needs to do is find a slight hill to sit on from max range and he's completely untouchable by anything in the base. Having fired from a height advantage, there is nothing anyone in that base can hit the tank with.
To give you an example, a couple days ago the TR were attempting to take Searhus from the VS.
Map of Searhus. It came to the point that we had taken Matagi and Akua, and were moving on to Oro and then Pele. Sitting along the rim of that volcano were tons of MBTs and BFRs, constantly shelling the area below. All of those vehicles were well out of range of the base, and the VS had no recourse but to bring the fight to the tanks if they wanted to defend themselves. But at the same time, those vehicles weren't even in render distance of any enemies at the base. They could see the facility but absolutely nothing within it. All of their kills in that base were designed entirely around luck, and TR only actually took the base when they realized they would have to leave the rim of that volcano and actually go down there en masse.
Defending yourself from bombers trying to do the same thing in PlanetSide 2 would actually be easier than this scenario, given that the VS would've actually had the ability to bring their own vehicles to the fight without the threat of any enemy ground-based AA. It would be purely an aircraft vs aircraft dogfight with zero ground interference.
3) I can't really tell if you're being hyperbolic or just unrealistic. You're describing a scenario that can already take place in PlanetSide 1. Imagine an aircraft approaching a base at flight ceiling, diving down to make an attack, and then ABing straight back up into the air and away from the base. All you'd be changing between PS1 and PS2 is that instead of being 20 meters further from the base horizontally, you'd be 20 meters further from the base vertically. Either way you're getting out of range of ground-base AA at an identical pace, just plotted on a different axis.
If you're saying that the ground-based AA are still reacting too slow to respond to you, then please tell me what empire you're fighting against, because as a pilot they sound like heaven.
4) This is where I start to think you're using too many fringe hypotheticals as cons. It feels like you're saying, "This could cause problems, lets not try it." instead of saying "Yeah, that could be interesting, but we have to make sure we balance it correctly."
I'm trying to make the argument that high-altitude aircraft don't need a ground-based counter. Their effectiveness is so compromised and there are other methods of air-based countering that its unnecessary for ground forces to always have a hard-counter.
That said, I certainly cede the fact that without testing, no one can fully anticipate every eventuality, myself included. That's why I'm open to the idea that if high altitude aircraft do become slightly too powerful, there is always the option of
special high altitude AA that is rare, and offers a "light touch" just to keep high altitude aircraft in check.
But it appears like you're making the argument that before its even evident that high altitude AA is necessary, that its already underpowered because its too hard to obtain/switch to/understand. It seems like you're making some preemptive objections when its way too early for them.
5) This is another aspect of high altitude that I think really balances itself. Bases already have higher defenses. Its the natural gathering point for aircraft, whether to repair or rearm, or just form up and move out together. For that reason, you're going to have to break the door down and truly own the skies before you can even consider high altitude bombing without getting swarmed by enemy aircraft. You're flying an slow moving target with two players inside just begging to get picked off. Aircraft are already going to swarm you.
However, once you begin trying to bomb outside of a base in open-field engagements, you don't have to worry about that constant threat of enemy aircraft. But you do have to deal with the fact that your targets are a lot less bunched up. They don't have facility walls to contain them anymore. You're also dealing with a much more mobile force. Tanks are constantly pushing out and retreating to repair, infantry are pushing front lines and trying to grab the next hill or rock for cover. Trying to bomb from maximum altitude is a practice in insanity. Nothing you fire at is still going to be there when your bombs hit the ground. Like I mentioned above, people repairing tanks and AMSs out in the field have more time than they could ever want to pack up and move before your bombs hit the ground.
The only thing you're going to be crushing from high altitude is your own will to waste more time dropping bombs on empty fields.