What abilities should the commander have?

Good point indeed, the Commander shouldn't suddenly become defenceless once underwater.

I'd prefer good old jetpacks, and maybe not with orbital capabilities...

Another thing I'd like to see is an auto-option on the D-Gun. This is assuming that the D-Gun consume a lot of energy, but has a medium ROF (a few seconds, not a few dozens like some artilleries).
The idea is that in early game, you don't want to do that. Your D-Gun can be a great help and a life-saver, but its energy cost makes you want to be sure to use it only when really needed. But in late game, when your economy is far more robust, this would relive you from a big micro hassle while you have far bigger armies to manage.
It would need to take into account your energy reserves and production, ideally with a priority toggle. It would also need to be smart, not wasting it against a lone scout while a raider swarm or a heavy tank is approaching right behind it.

Rocket Jump, D-Gun style?

Yep that's exactly it! Wouldn't that be awesome?

I still think some big unit in the game should have the ability to shout a loud taunt/roar before it devastates someones army/base.

The function of the Dgun is to make the commander effective against everything. A commander so equipped is impervious to practically any single unit trying to kill the commander. However, due to the high energy cost to fire, a large number of small units remains relatively effective at taking on the commander, meaning you don't want to just roam about the map with it.

Commanders in TA were actually quite squishy due to the usability of the Dgun. Compare this with ACU's in SupCom, which are extremely tough, but more reliant on a constant dps attack than their dgun analogue due to its much higher energy cost and significant mandatory cooldown.

The linear splash damage was presumably added to create a certain level of micro for the one unit on which it might be justified, and enabled skilled Dgun users to survive battles where other players would have died.

The dgun is not strictly necessary for a commander. However, the principle of having a relatively squishy commander that needs to be protected is a good one. ACU's in SupCom are so durable that they are often used as combat units with little risk. Especially early and midgame, there is essentially no risk to using your commander to fight T1 units, or even small numbers of T2 units. Under these conditions, it is even optimal to use your commander to tank damage for your combat units, destroying some of your enemy's army while losing nothing but your ACU HP, which regenerates for no cost. Even if the enemy commander is present, it is unlikely that your ACU will be destroyed.

That's really... really wrong.

About 20 t1 tanks will splat an unsupported ACU no worries. T2 units are a much bigger worry.

If he has 20 tanks, so do you. Your 20 tanks plus your ACU will crush his 20 tanks alone, and if their tanks are shooting your ACU, your casualties will be very minimal.

You are correct that you can royally screw up and die by fighting with your ACU. Especially if you don't micro and get killed by mobile artillery in seconds. However there is really nothing your opponent can do to force this to happen, and no real reason why it should.

Sure there is. Plenty of replays to watch to prove you wrong.

Actually... if you upgrade your factory you won't (the time+resource cost of upgrading a land factory from T1 to T2 will put you back by 20 tanks).

I think it would be necessary to give the commander the ability to attack any unit type, especially in galactic war. If you have to wage a war when the enemy might start with and upper hand.
Escape Pod just seem like a bad idea to me, they negate the value of the commander, and cam make them a walking Nuke.

There's a mod for SC called BlackOps that I thought did it quite well, it gives the commander more upgrade options than standard SC, where you pretty much always picked the same ones

Does nobody else want the commander to have the ability to pick up smaller enemy units and fling them back at the enemy?

I'd be disappointed if it wasn't expected. Disintegration gun, light rapid laser and cloaking if you have the energy for it.

I don't think the cmdr should get anti air at the start. But as a later game addition. You don't want to ruin those awesome early freedom fighter battles now would you?

I think the Commander should have a small set of very well-defined abilities. The commander should be a fearsome foe in battle, and should be able to create a base quickly. Anything else and he becomes either too powerful, or a jack-of-all-trades and master of none.

I can see a Commander in the midst of a battle, reclaiming the life out of some near-by enemy k-bots (which it should do automatically if it is in a battle) and killing stuff with it's laser, while growling like the Hulk, maybe even the good ol' EMP/Neutron ability to disable nearby units (even friendlies?) to escape from battle. Ninja vanish!

A D-Gun should definitely be available from the beginning. However, I do not like the idea of teleportation. I don't know how well that would go over if the commander teleports away from the middle of a battle. I think it might become too OP and put too much emphasis on the Commander, and would decrease the importance of other units. If anything, I would support short flight for a possible quick getaway (that is, if a new Commander can't be constructed after the first is destroyed).

I agree with the idea that the Commander should be able to build a base quickly and also, perhaps a sort of minor passive ability that gives friendly units a small attack bonus or something when in a certain range.

I think that teleportation would be an excellent tool. Teleporting away in the middle of the battle would make ACU sniping harder, which is a win for gameplay overall.

I'm not a fan unless the end of game hide & seek and suicide-bomber antics can be mitigated somehow.

I think that any additional commander abilities should be put in as modules you need to pay for, like in SupCom1.

While SupCom2 went overboard a bit on adding more abilities, one of the key problems it had was that it removed choice between the abilities. Instead of customizing the commander for your purposes, it just turned him into a DPS machine.

I always in SupCom1 liked getting the pod upgrade on UEF ACUs because I felt that the added construction and assist speed was useful, especially since I always kept my ACU back working instead of risking it as a combat weapon. I just built more tanks to make up for it not being on the field, which was easy to do with the extra assist from the shoulder pod bot.

I think the commander should not be a overpowered Hero Unit. Yes in the beginning it is possible to outrank the normal units, but to give them enough power to outrank even T3 units, no good idea. I like the game-play in FA where the ACU was able to shoot down T1 but had problems with T2 and even upgraded with laser beam it could not match T3 units.
Giving the ACU too much power it would be a high risk hero unit at the front line and the strategy stands and falls with the performance of this single unit if used. And last be honest which commander would place his life at the front if there is the possibility too die?

That's easy to solve: Give it a cooldown, limited range, and energy requirement.

Alexander, Charlemagne, Richard I... Many successful (and less successful) commanders did so across History...

Now, gameplay-wise, the problem with obsolete Commanders is that the only strategy with them becomes hiding them somewhere. And having one dominant strategy is not good for a strategy game.