But only one weakness per sovereign. So you then lose the opportunity to take other weaknesses that may be more suitable to your ruler/race and your way of playing. For example, if I'm using a Pariden-like ruler who focuses on magic and ranged attacks, Clumsy is a better fit, etc.

some of the weakness's aren't 'strong' enough not to take at all times.  The above points on Cruel and Clumsy fit that description.  You then are able to get an extra design point to put into something really nice, which sort of ruins the balance.

I wouldn't mind seeing the weaknesses get a bit stronger so that taking one really does hurt - but just enough that it's worth taking for that extra point in something else.

With ranged weapons, Clumsy should offer a chance to randomly shoot an ally and if the hero is by himself, then he shoots himself. Hilarity ensues.

I think taking Might and Weak together is a waste, and you're nerfing your sovereign by doing so.  If you want to max your sov's attack, you should take might and the weakness shouldn't drop that.  If you're going for more of a caster build, then you can take weak, but you wouldn't bother taking might.  If you could take as many weaknesses as you wanted, sure, it would be a flaw, but since you're limited to one, you're just limiting potential by taking the two together.

...And so does the player ignoring Clumsy unless they're magic wielders, only. Though if we take this to its logical conclusion, then Clumsy should also cause the ruler to occasionally target their own troops with attack spells, enemies with beneficial spells, and themselves with maluses. Hilarity, and no more Clumsy.

I don't think this qualifies as a bug.

Personally, I don't see the point in taking a trait that directly weakens another trait, seems counterproductive. Thus Clumsy is my typical weakness of choice, or sometimes Cruel, if I'm not using Rebels as the faction weakness, and depending on the Path I plan to follow.

It's not a free +1 attack.  You're using a trait point you could be using for something else.  When you take a weakness you get a trait point to spend on ANYTHING.  You could advance one of your spell schools, or take one of the traits with full benefit.  If you want extra attack, take one of the other weaknesses like -20% spell resist and get the full 3 attack in exchange for something that rarely matters.  You can't take another weakness to get another trait point.  I don't think you understand this.

It's still a weakness because it is weakening the Might trait, I would never choose this combo.

If I want a free +1 attack, I'll take Cruel. That lets me pick another, potentially more useful, trait, and +5 unrest in every city is barely noticeable and easily negated - just get a Commander specialized in Administration up enough to get Administration III and the malus is gone, or just ignore the penalty. If I want to get free attack bonuses, I'll take Might and Clumsy, because the penalty from Clumsy is so easily evaded that it almost isn't a weakness, and +3 attack greatly outweighs the chance of hitting your own units in melee, especially if you go for an archer build, in which case Clumsy can never trigger (unless you for some reason decide to equip your archer with a melee weapon), or I'll take Might and Cruel, for the same reasons as I'd take Cruel for +1 attack given above.

Beyond that, I'd rather take something like Brilliant or Tactician over Might, because my preference in champions is more Field Commanders and Mages than Warriors. Even when I go in for warrior-type champions, most of the damage is coming from trained troops anyways, since there are more of them and I'm not as concerned about losing them.

The point is, though, that if you're going to min-max for something, you pick what you're trying to maximize. If you want to make a great warrior-type sovereign, then there are better ways to go than Weak + Might. If you want a great Commander sovereign, then there are better traits to take than Might, and you probably want at least Air I, and possibly Water I, for Haste and Slow, which are great support spells with very low casting costs, and most enemies don't have enough spell resistance for it to be too difficult to get Slow to stick even with a relatively low-level commander. If you want a great mage, then Might has no real use for you except possibly in the early game, when you probably will not have the mana income for much spellcasting, and this stage doesn't last long enough that I'd consider it worthwhile to spend a weakness to gain a trait to get a net of +1 attack. If I'm that desperate for additional early attack, I'll either take Cruel and pick something that more directly benefits me as a caster (like Brilliant, Attunement, or Scholar) or I'll go for Might and a weakness that doesn't kill most of the benefit of taking Might. Moreover, magic tends to provide ways to get around unrest penalties (unrest reduction from Death and maybe Life, bonus production from Earth, bonus income from Air (allowing lower tax levels or fewer cities for similar income), bonus research from Water, better troops from just about any of them (allowing fewer troops, which permits you to spend less time on training), better troop conservation from Life (also allowing you to spend less time on training)).

In the end, though, the only time that +1 attack on my Sovereign is going to be helpful to me is right at the beginning of the game, when I don't have the mana production to support lots of spellcasting and don't have the economy to support large armies (or rapidly replace loses). After that part of the game, I should have large enough armies that my champions are kind of insignificant, I should have enough mana income to cast at least one or two good spells per battle, I should have found a +1 attack book or a better weapon, or something else that makes +1 attack on the sovereign insignificant. If you want to min-max for an easy early game, there's better ways to do it (especially since as long as it's in the early game, your armies are small enough that working around the penalty from Clumsy is trivially easy, and +3 Attack from Might and Clumsy is far better than +1 Attack from Might and Weak - early game, you're usually looking at no more than 10 defense on enemies and about 10 attack on your sovereign, so +1 attack is roughly a 10% damage boost while +3 attack is roughly a 40% damage boost), and if you want to min-max for an easy late game, then +1 attack is almost worthless.

I think your timeline is pretty close to accurate. Wasn't "Weak" just recently changed from a weight capacity weakness to an attack penalty when encumbrance was removed?  I think the current interaction between these two traits was not intentional. 

There is only a cost if you intended to take another weakness. If not, there is no reason not to tack these two on. I rarely take weaknesses except for "Rebels" sometimes. I don't abuse the might/weak freeby (personal choice), but really if I or other players were playing optimally in that situation, you would tack it on every time, and have this bizarre mighty-weak sovereign with +1 attack.

*facepalm* its all good jshores, some people like myself understand the point your making.. i suppose the counter as others have said is the using up of the weakness.

horses for courses