The minor issue is with the commands:
+Shoot2 shoot lasers/ion cannons
+Shoot1 shoot rockets/missiles/swarms
+Shoot3 lay prox mines/lightning mines
Weapon1 select lasers as active for +Shoot2
Weapon2 select ion cannons as active for +Shoot2
Missile1 select rockets as active for +Shoot1
Missile2 select homing missiles as active for +Shoot1
Missile3 select swarm missiles as active for +Shoot1
Mine1 select prox mines as active for +Shoot3
Mine2 select lightning mines as active for +Shoot3

These work as detailed, but the semantics are a bit out of date with what is possible in game.

It would be nicer to have the following commands/semantics:
WeaponGroup<n> <m1> <m2> ... <mk>
which sets weapon group n to mean weapons m1 through to mk where each mi is an index to the weapon as it appears in the ship ports install list. For example, on a Vulture,
/WeaponGroup1 1 3
would bind weapon group 1 to the front and right small ports, while on a Ragnarok,
/WeaponGroup3 2 3 5
would bind weapon group 3 to the left and right small ports and the rear large port.

(GUI note, maybe put a number next to each weapon in the GUI to make the mapping obvious.)

+Shoot<n>/-Shoot<n>
or alternately
+Shoot<n>/+Shoot<n> 0
which starts/stops firing weapon group n. (I prefer the first, but the second is more consistent with other game commands.)

For example:
/bind LMBUTTON +Shoot4
would bind the left mouse button to the fourth weapon group.

This lines up more with the way the stations present the info, gets rid of a layer of indirection in the weapon semantics and simplifies things for the player, who can now bind keys for setting up his/her weapon groups. Also, it hopefully shouldn't be a very difficult change, as weapon groups are already there, and there's already code to fire them and to change them.

*edit*

We also need a way to select the empty set of weapons for a WeaponGroup. It would seem reasonable to make this "/WeaponGroup<n>" on its own.

If we actually want to be able to print the weapon group, which seems odd, but not entirely unreasonable for testing purposes, then "/WeaponGroup<n> print" would perhaps be an effective syntax. I don't know whether having this feature would actually be useful though. Later on, perhaps when the cvar support is expanded, we'll want this info available through cvars, for sure. Just printing it is not terribly useful except maybe for testing purposes (but you could just shoot, anyway).

Some people have (outside of forums) expressed a bit of confusion over how this works, or that the system would be more confusing than what we have. It's really not.

The idea is that the WeaponGroup<n> commands would change your weapon groups (just as you currently would in-station) and the +Shoot<n> commands would fire those groups of weapons.

It's much simpler than what we have, but I think it opens up many more possibilities, and it only really affects those who were already using binds/aliases to control their setup. For those who weren't it would be a very minor change. (Except that they'd now be able to bind a few more firing commands to keys in the config box if they wanted.)

I would like it that each number pertained to a weapon config rather than assigned weapon ports. Suppose you have a vulture with dual Gauss. Hitting one would mean both Gauss are bound to the primary fire. 2 would mean one is primary, the other is secondary.

Or if you had a Hornet with a gat, 2 tachs, and a flare.
1-would mean the gat and the tachs are primary, flares are secondary.
2-means gat is primary, tachs are secondary, no flares.
3-means . . .

I think this would lead to some cleverer weapon configs than binding keys to "missiles and mines" or the present system.

For the first config under this scheme, the vulture, you'd set it up as follows:
/alias ConfigOne "WeaponGroup1 1 2"
/alias ConfigTwo "WeaponGroup1 1; WeaponGroup2 2"
/bind 1 ConfigOne
/bind 2 ConfigTwo

or in the case of the Hornet, somehow I don't think that a gat would fit in those small ports, but I'll assume you misspelled Gauss. :)

/alias ConfigOne "WeaponGroup1 1 2 3; WeaponGroup2 4"
/alias ConfigTwo "WeaponGroup1 1; WeaponGroup2 2 3"
/alias ConfigThree ...
/bind 1 ConfigOne
/bind 2 ConfigTwo
/bind 3 ConfigThree
and so on.

In both cases, you'd then bind your "primary fire" to +Shoot1, and "secondary fire" to +Shoot2 and things would work as you described.

You could even make use of more WeaponGroups, for example to avoid making the flares completely unavailable in the second config, do /WeaponGroup3 4, then +Shoot3 would fire them.

One nice thing is that you could store all these up in a config file for each ship you like to fly, and /load it with a key when you get into that ship. No fiddling around in the station, or forgetting to, which is even more annoying. (Or maybe you could even use a trigger to call the /load once we have those.)

I'm going to start thinking about how a decent GUI would look on top of this framework. The current station GUI is enough, but not half as flexible as doing this yourself. I'd like the GUI design to expose the basic functionality here, (you can't expose all of it, since you could do very complicated things with aliases) and also make it reasonable to have automatic WG config in the station that remembers your saved setups and binds them all for you. The nice thing is that if you actually want something as basic as the old Ions/Missiles/Mines system back, it's not hard to get here, and can be done entirely at the level of binds, rather than being hardcoded.