In our games, we've added two class features to the monk that take care of the Flurry of Misses and M.A.D. They may have been yoinked from elsewhere, but if so it was so long ago I forget. Sorry if one or both are your idea.
Inner Strength (Ex):
When a monk of 3rd level or above attacks with an unarmed strike or a special monk weapon, he can substitute his Wisdom bonus for his Strength bonus to modify his attack roll (if it is better). He still uses his Strength to modify damage.
and
Channel The Void (Su):
Starting at 4th level, a monk can enhance his own unarmed strikes and unarmoured AC. This works like the Craft Magic Arms and Armour feat except that it only works on the monk's own body. In place of spending time crafting, he retreats to a secluded location (often a cloister) for meditation. In place of spending gold on materials, he makes an equivalent sacrifice of material wealth (to the poor, a donation to a temple, or something similar).
The monk can apply enhancement bonuses and special weapon or armour properties, but must make a Concentration check with a DC of 15 + spell level in place of any spell prerequisites he fails to meet. Success means the enhancement works, failure means it stalls for one day. Three successive failures ruins the attempt and half of the sacrifice is wasted.
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These two features address the core of the monk problem - weak attacks and MAD.
The first reduces MAD by removing strength from the mix, without making it a complete dump stat (it still modifies damage). With one less ability score to pour resources into the monk can be more effective at hitting things. Sure, it makes Wisdom uber for monks. But that is fine by me, since it reflects the whole "don't judge me by my size" thing flavour-wise and requires three full levels to get so it isn't a no-brainer for clerics and druids to dip. Why 3rd level? To shift it away from first level, and because Still Mind isn't such a cool power that it couldn't handle a bit of company.
The second improves the monk's ability to hit and gain cool ki powers without relying on external factors such as magic items and spells. Why 4th level? Because thats when a monk gets Ki Strike, and that's when the
good samurai class (the one from OA

) gets their similar feature of Ancestral Daisho. Oh, and it gives a monk a reason to take the thematically appropriate Concentration skill.
Both make for good flavour as well as a quick workable fix.