I don't think there is much of a balance issue to pooling the feats and letting the monk choose one. None of them are over powering. I agree I just think that the authors didn't give it much thought. They did make flurry and Ki strike better.
I have never thought of monks as weak even in 3.0. They are a more difficult class to play certainly, and they are not the Hack and Slash kung fu masters of the movies.
The bigest problem the monks have I see are this.
1. They are percieved to be a main combat class and they are not. They are a support class. Low HP and Low BaB compared to other warriors sees to this. Flurry of Blows exagerates this problem with the extra attacks but at -2 to a already lower BaB.
2. They are overly stat dependant more than any other class. They are a combat centered class but thier abilities depend on having high scores in many abilities STR for hit/damage, DEX for AC, WIS for AC and abilities tied to feats IE stunning fist DC, Con for survivability, INT for Skills, CHA is their only dump start.
Over the years I have learned a few tricks to play monks with any success.
1. Forget about Kung Fu movies
2. Arrange your stats in this order: STR, DEX/WIS (High dex if you are taking combat reflexes at 2nd) Con, INT, CHA. Strength is the most important stat. Most people sink their highest stat into DEX as it seems like the proper choice. But with the low BaB and no options to increase damage (specialization, sneak attack etc) you need every bit of bonus to STR as you can get. It is alot easier to get your AC higher than it is to get your Damage potential Higher.
Monks biggest problems are that they can't hit anything, or if they blow a feat on Weapon Finesse they can't damage anything.
3. Choose feats wizely. The "Spring Attack Chain" is bad for monks because of #2. You will have a decent AC with dex and wis bonuses, and eventually magic. Feats are more precious.
4. Grapple Grapple Grapple. Monks rule in this area. Another reason for high STR. If your STR is your highest score you don't have to blow feats to get your attack bonus higher. If you can use OA or the d20 monk supliments there are a bunch of feats that make this an even better option.
You can make a grapple attack as a TOUCH ATTACK. If successfull you deal unarmed damage which is higher for a monk than anyone else. High STR is needed here. too for damage and grapple checks. And for visualization not all grappling is done on the ground, Chin Na, Judo, Akido, Ju Jitsu among others all use 'grappling' techniques and are not 'wrestling' This is the monks best combat option against humanoids.
5. Read up on other tactics other than attack. There are alot of options. Trips are great in 3.5 as getting up from prone draws an AoO. Combat reflexes comes in handy hear as well. And there are other options. Combat IS movement. Monks have the best movement capitalise this. You are very good against humaniods. Trip the leader and keep him down, you can move better and get at the leader easier than anyone else. With Improved trip you get a free attack when you trip.
The best thing I can think of to fix the monk would be a 2 step process. 1. Make the bonus feats a pool you can choose from, adn add weapon finese to the pool. 2. Make a new feat that allows your WIS bonus to up your damage instead of STR. Basically your CHI or inner power increases your damage rather than your STR. This makes mush sense, and fits internal styles better than high STR.
To bad my dm won't go for it, no player created feats allowed

so I have to throw the best score in STR and play alittle out of type.
If you had a this feat lets call it Chi Focus, pre req BaB +1 Wis 14 benifit you have learned to focus your chi, your wisdom modifier now adds to damage dealt instead of STR; Then the monk would be less stat dependant.
This 2 step process would allow the monk to be better in combat at the cost of 2 feats, but would make it MUCH less stat dependant. You could also make old masters who are very good but not strong and they would be feared. These 2 subtle changes would make a world of differeance