ORIGINAL: Sunburn
AI crews seek the optimum altitude (fuel consumption wise) for their selected speed, either picked on their own (mission AI etc.) or manually dictated by the payer. If it's 40000ft, that's how high they'll go.
If you think the optimum fuel consumption happens in a different altitude for the given throttle setting, please have a word with the DB authors (Rag & Paul).
Don't bash the game because you disagree with the numbers.
Forget about fuel efficiency and all that crap. That has nothing to do with that. Any strike aircraft strolling into harms way at 40k feet is going to be a dead aircraft, unless they are utilizing state of the art stealth technology and/or have ample support allocated like SEAD/Jamming/AAW Escort aircraft. Not every mission is going to have air supremacy and/or ample support thus making ingress/egress altitude irrelevant. The whole issue here is survivability and radar detection. Strike aircraf, in many missions, are going to strive to stay below radar horizon as their "support". The mission AI has been given zero intelligence, nor does it allow the player to create a mission and "program" the AI to conduct a smart mission. This can easily be solved by adding ingress/egress options to the mission editor (among other options to allow the player to create "smart" mission). Right now the mission editor seems to launch everyone at 40k feet and away they go and away they return, the few that survive. Bottom line, Command in its current state requires manual control of strikes to have any chance at survival. Unfortunately, the manual control capability needs development itself.
I'm not crapping on the game, I'm just pointing out what many experienced naval simulation players are thinking are have already said in other threads. Just come clean and say "yeah, we know 40k feet on all missions isn't what we want and we're working on it". We respect that. Don't defend it with stuff like this please. You might get away with it on the "newbies" to the genre that don't know any better, but you aren't with the Harpoon crowd, and that's the crowd that enthusiastically ran out and paid $89 for Command on launch day.