It seems that the only weapon for a monk worth running around with is handwraps. On occasion, it may be worth your while pulling out some vorpal kamas but for the most part you will be ridiculed if you wield anything besides handwraps.

Some of the reasons for handwraps being so much better than other weapons:
Increased attack speed on unarmed attacks
- No str penalty for HW offhands
- 2d10 fist damage
- Many monk special attacks only work unarmed
- Monk weapons have terrible critical profile (20/2x)
- The weapons which have slightly better crit profiles (longswords/shortswords) require sizeable investments (WSS, ninja enhancements - although this has other perks
- No greensteel with HWs, but ToD ring damage

I have the following radical suggestions in mind to help balance:
1. Make TWF feats no longer work with unarmed attacks (more on this in a sec)
2. Remove two monk bonus feats (lvl 1 and 6)

So much for the nerfs. The idea now is to implement double strikes to up the rate of procs to TWF levels

3. Flurry of blows to grant double strike bonuses at monk lvls 3 (5%), 9(5%) and 15 (10%) when centred and wielding monk weapons
This would be on top of the bonuses flurry currently grants. I selected the break points with the aim of avoiding abuse via multiclass PREs and backloaded to avoid any possible acrobat/staff exploits.

So far, we've made up 20% of the 80% that the TWF chain currently grants at higher levels
4. Introduce selectable feat 'Improved flurry'
+ Selectable as monk bonus feat (lvl 2)
+ preq: BAB 1, Dex 15
+ Provides bonuses to double strike at levels 2 (20%), 5(10%) and additional 10% every 4 monk levels thereafter (all the way to 60% at lvl 17)
My current thinking is that one feat provides 5 tiers of bonuses, although it may be better to split into 2 (another feat at lvl 9) for balance purposes although if an additional feat was required, would probably only remove one monk bonus feat selection to begin with.
+ only active when using single handed monk weapons, with no off-hand weapon equipped

Created the following table for pure monks, showing the proc rate with current TWF feats taken as early as possible and the new proposed system with F(lurry) with 3 tiers and I(mproved) F(lurry) with 5 tiers:

Lvl Current Proposed
1 40% TWF 0%
2 40% 20% IF I
3 40% 25% F I
4 40% 25%
5 40% 35% IF II
6 40% 35%
7 40% 35%
8 40% 35%
9 60% ITWF 50% IF III, F II
10 60% 50%
11 60% 50%
12 60% 50%
13 60% 60% IF IV
14 60% 60%
15 80% GTWF 70% F III
16 80% 70%
17 80% 80% IF V
18 80% 80%
19 80% 80%
20 80% 80%

(apologies for table formatting - haven't quite figured that out yet)

The proc rate lags behind the current TWF system, although you only have to take 1 feat to get the benefits, and it applies to more weapons

Note, the system wouldn't preclude you from taking TWF - they still would work with two weapons. In fact, taking TWF feats and dual wielding kamas would net you 20% proc on main hand, and 80% proc on offhand. Alternatively, you could just wield one kama, and use the IF feat to net you 80% proc on the main hand - you have options.

Ultimately, unarmed remains unchanged but monk weapons will have 20% proc to main hand, and up to 80% if single weapon wielding.

The next two proposed changes are to make swords more viable:

5. Remove weapon focus requirement from WSS
Currently not very desirable, requiring two pre-req feats. Only have the one pre-req may make it appeal to elves or humans.

6. Allow crit ki bonuses on all crit rolls
i.e. even if the mob has 100% crit resistance, kind of how burst effects proc. One of the appeals of spending an extra feat to use swords as ki weapons should be the increased crit range with the possibility of building ki up faster although this is negated on crit immune (common) or resistant (less common) mobs. Even when mobs aren't crit resistant, they are often stunnable via SF, which makes the increased crit range of swords moot. The suggested change improves all styles, but sword styles the most.

Finally, a suggestion for ranged although will note many people have already suggested changes for the following enhancement:

7. Ten Thousand Stars enhancement
+ 20 sec duration
+ 40 sec cooldown (i.e. 20 sec down time)
+ cost 10 ki
+ operates like many shot for shurikens (i.e. volleys of stars, BAB determines volley size)
+ each projectile throw uses 1 ki (i.e. volley of 4 would use 4 ki)
You can still throw multiple shurikens if you are still within the 20 sec duration
+ TS ends if non-shuriken weapon is equipped
+ shuriken hits do not build up ki (as it is currently)
It has less downtime than manyshot for bow users, but shurikens are a lot less powerful than arrows. Also don't expect to have much of a ki store after using it - you'll need to mix up some melee to get the ki to reactivate it.