This is why you need to have powerful abilities.
Incidentally, a fighter can't purchase 6 ranks in Use Rope until... level 9, I think. You really might want to drop that requirement.
By the way, you need to have better fluff. Might I suggest the following?
[sblock]The Master of Chains is a canny opportunist whose intimidating presence is capable of inciting hardened soldiers into a panic. Using mystical martial techniques first pioneered by chain devils in the early days of the Blood War, a Master of Chains can gain an unnatural degree of control over his weapon, enhancing its damage potential and even allowing him to use it as a weapon.[/sblock]
In addition, I've been looking over the class design and have some suggestions.
[sblock]
Requirements:
Alignment : Any nongood
BAB +6
Intimidate 9 ranks
Exotic weapon Proficiency: Spiked Chain, Combat Expertise, Improved Trip, Improved Disarm
Hit Dice: d10
Class skills: 4+Int/level, Balance, Bluff, Climb, Intimidate, Jump, Listen, Profession, Spot, Swim, Tumble, Use Rope
Level Base Fort Ref Will Special
1st +1 +0 +2 +0 Punishing lash, Combat Reflexes
2nd +2 +0 +3 +0 Scare, Immunity to Fear, Chain Armor
3rd +3 +1 +3 +1 Greater punishing lash
4th +4 +1 +4 +1 Constant Vigilance
5th +5 +1 +4 +1 Tactical Expertise (+2)
6th +6 +2 +5 +2 Superior Chain Armor (Su)
7th +7 +2 +5 +2 Sweeping Strike
8th +8 +2 +6 +2 Tactical Expertise (+4)
9th +9 +3 +6 +3 Spiked Chain Armor (Su)
10th +10 +3 +7 +3 Cheap Shot
Combat Reflexes: The character may now make additional AoO's as per the feat but the amount of additional AoO's is his dexterity modifier, or one-half his strength modifier, whichever is higher. If the character already has the feat, he gets a extra AoO.
Clarify if this ability counts as the Combat Reflexes feat for qualifying for prestige classes and feats.
Punishing lash: If the MoC kills someone, he may now use the same attack against a other adjacent enemy, but this only does half damage. This is limited to one extra hit per round.
This ability is weaker than the Cleave feat; "If you deal a creature enough damage to make it drop (typically by dropping it to below 0 hit points or killing it), you get an immediate, extra melee attack against another creature within reach. You cannot take a 5-foot step before making this extra attack. The extra attack is with the same weapon and at the same bonus as the attack that dropped the previous creature. You can use this ability once per round."
I'd just grant the Cleave as a bonus feat and be done with it, or at least copy the text.
Greater punishing lash: Same as 'Punishing lash' but the MoC may now take a 5ft step between each swing. If he also kills his second enemy, he may lash at another target. The number of extra attacks is limited to half his strength modifier per round.
Scare (Sp): A Master of Chains may induce fear into his enemies as per the Fear spell. The DC is equal to 10 + 1/2 his ranks in intimidate + class levels in Master of Chains. This ability may be used once per day for every level the character has in Master of Chains.
A Master of Chains is likely to have a relatively low will save, which means he could easily be disabled himself by an enemy's fear effect. Perhaps he should get immunity to fear? It's not a very powerful ability (Paladins get it at level 3) and it makes sense that someone who focuses on scaring the pants off of others should be resistant to fear himself.
Tactical Expertise: A Master of Chains gains a +2 bonus on his Trip and Disarm checks. This bonus becomes +4 at level 8.
Renamed to Tactical because Improved Expertise sounds too close to Improved Combat Expertise. Could get confusing.
Chain Armor: A Master of Chains may use 20 feet of chains to reinforce his current chain-based armor. He gains a +1 AC for each class level in the Master of Chains.
Superior chain Armor (Su):The armor of the Master of Chains user now fully consists of chains. He he looses the benefit of his already equipped armor, in exchange for the ability to will the armor around him and equip it in 1 round. After equipping this armor the chains keep moving around his body, granting a extra +4 bonus to AC and the Light Fortification effect. This armor has no check penalty except for a -4 to his move silently check due to the noise the chains make whilst moving. This is a supernatural ability
What about dexterity bonus? Is it capped? How cone the chains are heavy enough to grant a bonus to strength but not incur armor check penalties? You might want to add an arcane spell failure chance since all armor has it, say of 20% or so.
Spiked Chain Armor (Su): The Master of Chains may now use spiked chains as his armor. As a free action, he may draw his weapon from his shifting armor.
A Master of Chains gains +14 to AC at most, along with the Light Fortification ability... but that's not going to cut it against a Hydra. Perhaps it might be a good idea to have Spiked Chain armor grant Medium fortification and enchantable so that it does not become obsolete later on.
Superior Strength: The body of the MoC strengthens itself due to the extraordinary strain it endures from the weight of the chains, granting the character +2 to strength.
The Warmind prestige class has an ability I think fits the Master of Chains much better than Superior Strength, called Sweeping Strike.
Sweeping Strike (Ex): At 5th level, a war mind gains the ability to make great, sweeping swings with a melee weapon. On each melee attack a war mind makes, he can choose squares he threatens that are adjacent to each other, and his attacks apply to creatures in those two squares equally. A war mind can use this ability on any attack, even an attack of opportunity or a cleave attempt.
A war mind cannot use this ability if he has moved more than 10 feet since the end of his last turn. If a war mind drops one or both of his foes with a sweeping strike, he can attempt a cleave normally; however, he makes only one cleave attempt per sweeping strike, even if he drops more than one foe.
This. Is. Awesome.
Constant vigilance: An opponent who enters into your threatened are must treat your threatened squares as difficult terrain, forcing him to move with caution.
Cheap shot: Any opponent that you threaten who takes any sort of movement provokes an attack of opportunity from you before they leave the threatened area. They are also unable to use the withdraw action to treat the square they start in as no longer threatened by you.
If so, you may want to alter the progression a little to space out the battlefield control aspect more evenly. I'd suggest having the Constant Vigilance ability towards the front.
[/sblock]
Cheers for the sweet suggestions!
Also forget the cross-class skills have halve progress... 
