Below are a few changes the groups I play with have made to the Monk class. We have been using these for over 2 years now. We have just really begun to play Pathfinder within the last month and found we went back to the old monk system we previuosly had. Hit ratio and damage seem to have always been a factor for us as well.
Monks no longer gain improved damage as they level with their unarmed strikes, but instead: They do 1D8 points of damage. Beginning at 4th level and every 4th level thereafter they gain a +1 enhancement to their unarmed strikes. A monk may trade a +1 enhancement for any one of the following properties starting at 8th level .... Brilliant Energy, Defending, Disruption, Flaming, Frost, Ghost Touch, Keen, Merciful, Mighty Cleaving, Shock, and Thundering. A monk now also uses a Fighters BAB table. Can only be used with unarmed strikes. Wielding any weapon, including in off-hand and special monk weapons, negates all benifits.
This is comparible to the Paladins Bond ability. Works well when stacked with fighters damage ratio and makes the monk more of a martial artist type character most people are looking for.
Also concerning Fists of Furry, we have also allowed a monk to take an exoctic weapon feat in non-two handed weapon and add it to the monk list. However, even Racial weapons such as Dwarven Waraxe which is a martial weapon for Dwarves, would still have to take the weapon as an exotic weapon feat in order to add it to the monks list of special monk weapons. Giving the fact it only adds one attack and cannot be increased like Two Weapon fighting (improved or greater giving more off hand attacks) this has not unbalanced our game play.
With the above changes we have found that monks make more use of weapons, but not so much as to lose the flavor of the traditional Hand to Hand masters.