Here are some suggested values:

Commander base trait

Unlocks traits that improve economy

-15% to Unrest in the city this unit is in

+1 to the army's Initivative

+ 3 XP/season when stationed in a city

Administrator I

-10% to Unrest in the city this unit is in

+2 XP/season when stationed in a city

Administrator II

-15% to Unrest in the city this unit is in

+3 XP/season when stationed in a city

Administrator III

-5% Unrest in all cities

+50% XP/season when stationed in a city

Adventurer's Guild

Stationed champions gain 4 XP/season

+1 Fame/season

Innovation

150 research

Commanders are by far the strongest sovereigns, especially if you take

- the race Tarth because their double attack is made with -15 % hit chance or

- the race Trogs because the juggernauts can attack several times until their goal avoids an attack and the juggernauts lose -15 % hit chance with each attack.

For both races the Commander ensures that they will always hit!

2nd reason: The bonus to initiative ist awesome! Attacking first (and more often) is the key to win a fight. So I can normally attack twice against high armor troops before they can do anything.

I disagree. Yes, the Commander who wants to be a good combat commander gets no immediate path from the path trait alone. But you'll need to level him to be good anyway (goes for all heroes), so I don't see it as such a big issue.

Personally, a level 5 commander is so much more useful to me than a lvl5 anything else. By level 5 he can have road building, and administrator I, and either admin II or merchant I, whichever I need more.

A lvl 5 commander like the one above never needs another level - i can swing him around to the neediest city at a time, and focus on leveling my combat heroes.

Not that I ignore the commander as a combat choice, too, it's just a different level up investment. He needs to get to at least tactician I and have the Command ability - but then he is a great addition to an army.

So to sum up my point, I find a lot of value in the Commander as-is.

I like Commanders. In fact, one of the cool things about this game is some people will say a certain type of champion/sovereign is a poor choice, and you'll find others who disagree.  So, I'm not saying you are wrong; for you, Commander probably is a poor choice. However, for some of us it's an excellent choice.

When you get a champion Commander (as opposed to your soveregin), it's an interesting game decision how much effort to you put into leveling him. I'll put him in my main stack with my sovereign for a few levels, but how high? If I could level him my camping him in a city, it would eliminate an interesting strategic decision. Come to think of it, I almost always make my first (level 1) champion a Commander, so how bad can they be?

If you pump out commander henchmen, keep them all in the same army with your sovereign, and get them to the xp bonuses as soon as possible, you can get them all past level 30 fast (and bring other henchmen/champions of mage or warrior path along with them).

Commander weak? certainly not, it is actually one of the best class if you already play the game hundred times.

If you are initiative focused, constant spam battlecry is even better than other class except mage that spam blizzard, a fireball mage is losing this contest easily against commander with battlecry. the gap is even further if the commander is leading a ranged heavy units (especially mage units, i say units, not champion).

If you have henchmen, due to henchmen champion doesn't split exp, you can have 3 henchmen commanders leading entire army full of mages in no time, all kind of enemy army will never act and will be slaughtered very fast due to battle cry spam.

In late game, if you have strong army technology, commander easily tops out other class, yes, even against mage with blizzard.

Its capability to make road is also a very strong bonus, both for defensive or offensive purpose.

Its exp bonus as noted by others above, is insane bonus, especially if your commander is a henchmen, because he won't drain exp, meaning no exp split.

However if you use commander for administrative purpose (meaning you take traits that boost research/gildar/unrest reduction), you certainly use commander in a wrong way. But i agree if a rework is needed for this administrative trait, especially the gildar and research one.

Two commander henchmen with maxed out "Tactics" traits will make any stack much deadlier.

Henchmen are great: build your own champions. The only problem is that they are REALLY good if you rely on them as a strategy, and it can trivialize the game. For instance, building 3-4 commander henchmen and giving them the trainer traits makes leveling up TOO easy.

Sions are just like henchmen, except they don't count as champions: when they die, they're dead, but henchmen just get an injury.

I've made two mods that create new faction traits allowing non-Altar or men factions to get their own brand of henchmen. Let me know if you're interested, I can link you.

I would tend to agree with this.  When you conquor a City, stationing a commander there for a few seasons can be just what you need to get some good construction off the ground, and their road building ability is very useful.  In an army, they give xp bumps to your whole army and a big boost to accuracy. 

Also agree with others that the traits that give small bumps to research/gilder are the ones that need reworking, since they can be overshadowed by a good conclave/town.  Those traits may be marginally useful early on, but later in teh game, they will be a drop in the bucket.

I also find that most other classes (except mages) get outgunned by their own troops later in the game making them seem somewhat superfluous.