Excellent points you do make Kyad, but you don't need all that targeting. I do suppose having a select thing would cause precious seconds, so putting it as L2 was a good idea on your part.
Now for a counter: You can remove five of the targeting and reduce it to Reticule, Subsystem, and Turret. If you need a target escort button, then you really are blind. How hard is it to point in the direction of what you're escorting, and just focus on that? You can also remove auto match and auto target. Target can be put in the menu, and auto match can be removed altogether. Select isn't menu, and start functions already both as menu and exit. That opens up select for use. This can be used as your match button. Afterall, match is a pretty simple maneuver from thumb to select.
Take counter measures and switch it with Afterburners. Having R3 as it can cause involuntary movement issues.
"Lack of camera controls"
Because this is just so important. Crossed off
"No advanced targeting"
Advanced targeting? If I haven't heard of it, it isn't required
"Lack of hotkeys"
Once again, you really don't need hotkeys
"1, 2, and 7 will have a major impact on multiplayer (because who buys a console game for singleplayer these days, right?
Anyone who bought Bioshock, Fallout, Deadspace, or anything Rockstar. They make excellent singleplayer experiences worth playing.
Make the dpad your shield management then, while shift does Primary, Secondary, Firerate and something else.
X, Square and Triangle become your three targeting modes, and Circle does countermeasures. Hold Shift and the first three become ETS.
"In order to use any command not on the stick or triggers, you must give up control of your ship and leave yourself dead in water"
Was this you when you first picked up Descent: Freespace? Everyone has that moment where you had to look at the keyboard to make sure you were about to hit that right key. Eventually, it becomes second nature and you didn't even have to think about it. In this case, it's the same thing, once you learn the lay of the land, it becomes second nature and no longer an issue.
"But this would already be used to talk to your fellow players, would it not? I'm sure Bob from Arizona (fictional person) doesn't want to hear you telling the AI to do something every 20 seconds."
We're talking singleplayer. Bob from Arizone (unless he's dressed in a green outfit creeping outside your window) won't hear you.
In the end, we've cut out what isn't required, and placed all the important gizmos where they need to be without Shift. Then we added the not so important gizmos on top of the shift. I rarely switch firing modes, and generally don't care too much about switching primary and secondarys. I set them up in the order of importance, or have them all the same depending on just what it is I'm doing.
More than likely forgot myself at one point, and am missing stuff. Conclusion though, you don't need to have auto target auto match available like that. You don't need all that targeting, ETS has been implemented as well as shield management, there are still buttons without binds on my layout, you don't require camera stuff, hotkeys and advanced targeting are also not required. Besides, hotkeys are meant for PC players anyhow, not so much console.
On the subject of the keyboard attachment, there you have it.
There could be a little note on the box saying "Best played with headset and keyboard"