First, I have to say that I don't understand the debate of poison versus lawful alignment. I could see people arguing good vs evil, but the opposite of lawful isn't illegal, but chaotic. You don't mean to tell me that a lawful evil character can't use poison?
Now, since others have suggested it, here's my take on how to "fix" the monk.
First, I'd do away with the alignment restrictions. I'm still trying to figure out the concept of a lawful drunken master.
I'd also consider getting rid of the multi-classing restricitons.
Next, while I'd keep the BAB at its current state, I'd open up the list of monk weapons. All simple weapons should be allowed, as well as several martial ones (short and longsword, but not greatsword, for example).
Now, as to the common low AC problem, I'd allow the monk to use light armor and shields. I've seen kung-fu movies with monks wearing a little armor or using shields, so I don't believe it's out of line.
Now, as to how the use of armor would work with the wis bonus to AC, my take would be to take a cue from the Iaijutsu Master from OA. Allow the wis bonus, but only when not wearing armor. It might seem a little unbalanced to some, but remember that the armor use would eliminate the need for the AC bonus of the class, which would be dropped.
Also, the ability to wear armor would mean that most players wouldn't pump up their wis to such high levels, instead focusing on either their str or dex.
Next, I'd do away with flurry of blows and the unarmed BAB, and simply grant the monk two-weapon fighting for free at first level.
I'd also open the class up to maximum customization. OA already allows monks to swap out certain class abilities in favor of certain feats. What I would do is follow the example of the Inkyo in Rokugan and make all of the abilities bonus feats.
Like the Inkyo (and fighter), these feats would be true bonus feats selected from a list and not a choice between an ability and a feat (this would allow the monk to focus on being a weapon user, unarmed fighter, or grappler, or try for a martial arts mastery found in OA).
Stunning attack, deflect arrows, improved trip, and quivering palm all exist as feats in the PHB, OA, or Rokugan. Also, slow fall can be dropped in favor of the option of taking the break fall feat from Spycraft.
Now, I'd address the much needed niche of the monk. Since the monk is all about mastery of the mind and body, I'd continue to allow monks their SR. Also, I'd not only allow them to keep their bonus against enchantments, but give them an equal bonus against illusions, as well (although, off-hand, I can't recall if illusion are covered in SR).
Finally, continuing with the concept of the monk's niche, I'd eliminate timeless body, tongue of the sun and moon, leap of the clouds, empty body, and perfect self and instead allow the monks access to a select number of spell at higher levels, much like the ranger does now.
These spells could only be cast upon themselves and also would be limited to physical and mental enhancements, such as jump, bull strength, spider climb, undetectable alignment, mind blank, etc..
This would allow the monk to perform superhuman feats of body and mind and simulate the Crouching Tiger, Hidden Dragon style of martial artist.
Now, while the spells would allow the monk a wider range of abilities, they would be limited in uses per day, as well as which ones they choose to use (much like spells, you may end up regretting taking jump, but not mind blank that day).
