Mind, I'm taking the Monk as is. No multiclassing, prestige classes, feats, alternate class features, etc. Just the stuff you get out of the box.
First, the basic stuff:
First of all, the 3.5 Monk is quite MAD. You need STR for melee atb and dmg. DEX for AC, since you can't wear armor. CON, because you're a melee class and need the hp. And finally WIS for more AC and to fuel some of your abilities. That's 4 stats that require at least some investment, as opposed to a Barbarian or Fighter, who could get by with just STR (and CON, but not dumping CON is a given for any class).
D8 hit dice, medium BAB and no armor don't give you much staying power in combat (without significant investment and using workarounds), so you're better off taking a more mobile flanking role in support of a beefier party member, like a Fighter, Barbarian, Paladin and some other frontliners. Which I'm guessing was the basic design idea. The lack of weapon proficiencies is not much of an issue, since you'll rely mostly on your fists anyway, only pulling out a weapon to overcome DR or maybe exploit a vulnerability. (Funnily enough, Monks are by RAW not proficient with unarmed strike, but everyone ignores that)
The skill points and skill list are actually quite nice, with multiple useful skill sets available. But since you're already MAD, you'll probably have little left for INT after the more vital ability scores, especially if you're using Point Buy. This will likely leave you the choice between being good at one skill set or mediocre at several, unless you build specifically towards being a skill monkey, sacrificing. You could have some diplomacy ability, but those rely on CHA, which is likely your dump stat. Also, Tumble is virtually mandatory so you can get out of a melee that's getting to dangerous, so that's down one skill point.
All good saves. No issue here. No other core class has that.
Now, abilities:
Flurry of Blows - the trademark Monk ability. Getting an extra attack is nice, but your medium BAB and the -2 atb penalty make it rather tepid at low levels. It does come more into its own at lv9+, when the penalty disappears, and at lv11 when you get a second bonus attack at full BAB. However, it takes a full round action. So no move action and Flurry in the same round, leaving you with just a single basic attack without any bonus dmg die if you move and attack. Not very conducive towards the mobile flanker playstyle.
Bonus Feats:
Improved Grapple or Stunning Fist - both can provide limited crowd control, but grappling has a chance of working against almost anything and can basically put a weedy caster out of play for the rest of the fight, whereas Stunning Fist plain doesn't work against many creatures.
Combat Reflexes or Deflect Arrow - extra AoO or cause one non-spell ranged attack to automatically miss per round. Even if AoOs are situational by nature, that's an easy win for Combat Reflexes. There's just more applications for it.
Improved Trip or Improved Disarm -
AC Bonus - WIS to AC, and unlike DEX to AC, you retain the bonus while flat-footed. You also get an extra +1 bonus every 5 lvs. Increases your staying power in combat. Not bad, although it likely will get outpaced by magical armor.
Evasion/Improved Evasion - always nice.
Still Mind - +2 bonus against enchantment. Nothing amazing, but I'll take it. Mind-affecting spells are a *****.
Unarmored Movement Bonus - the other Monk thing. Being fast is great for a melee class, especially a flanker. But only if you can also bring some hurt at the end. Unfortunately, Monks don't have any built-in ability to do that. Compare to the Scout class, who also gets a speed bonus and the Skirmish ability, which rewards moving and attacking with extra dmg die and AC (and also gets tons of skill points to get all the mobility skills and still have enough left for stealth and scouting skills).
Ki-Strike - your unarmed strikes gain special qualities, like magical, lawful and adamantine. Decent, but gets outpaced by magical weapons.
Slow Fall - reduce falling damage if a wall is present. Situational, but sometimes handy.
Purity of Body - immunity to disease, except supernatural and magical, and those are the ones that actually matter.
Wholeness of Body - healing equal to Monk lv x2 per day. Slightly better than a Paladin's Lay on Hands, but seemingly can't be used to dmg Undead. Still, free healing that doesn't take up spell slots is always nice.
Diamond Body - immunity to poisons. Situational, but not bad.
Abundant Step - Dimension Door 1/day. Good for utility, but the standard action leaves its usefulness in combat limited.
Quivering Palm - death effect attack with DC 10 + 1/2lv + WIS vs Fort save, once a week. The DC is somewhat decent, but targets the most common good save and at the lv you get it, many things you'd want to use it on will probably make it. Also can't be used against many creature types. Finally, just once a week. Many casters at the same lv can do the same multiple times a day, like Finger of Death, which is similar but ranged and targets touch AC.
Timeless Body - no penalties to ability scores from aging. Nice in a campaign with frequent and lengthy downtime. If not, probably won't come into play.
Tongue of the Sun and Moon - Speak with and understand any living creature. Great for a diplomancer. Comes quite late at lv17 tho. Some items basically do the same and can be obtained much earlier.
Empty Body - use the Etherealness spell for 1rd x Monk lv per day. Like Abundant Step, nice for utility, limited for combat.
Perfect Self - become an Outsider and gain DR10/magic. The former makes you immune to certain spell lines. Nice. The latter is nice against monsters with no inherent magical physical attacks. Not much against humanoids, who at lv20 play will more than likely have magical weapons.
My conclusions
The fluff makes the monk out to be a highly mobile unarmed melee combatant and the general outline of the class seems to follow that idea. Relatively low AC and medium BAB/hit dice indicate you're not supposed to stay in combat long, and the speed bonus, several class skills and abilities like Evasion, Abundant Step, Empty Body paint a picture of mobility. Flurry of Blows works the martial artist angle. But none of them synergize with each other. You can't run and jump into a flanking position and still Flurry. Abundant Step and Empty Body can get you in position, but leave you with nothing else to do. A lot of other abilities have lots of flavor to them, but many don't really make you better at any role you can fill, if they make you better at anything at all.
Speaking of roles, I think the main issue I have with 3.5 Monk is that it has the potential to fill several roles, but not good at any of them. You either focus on being decent at one or two things, dumping the rest. Or spread things out and be subpar at everything.
You know, some people like to make fun of the Bard, calling it weak because it is a jack of all trades, master of none. I disagree. The jack of all trades part is true, but the Bard is at least competent to great at all of them. Bards make for great diplomancers thanks to the synergy between their skill list and CHA-based casting with lots of Enchantment spells. Aside from that, they're pretty good skillmonkeys. They have arcane casting with pretty good (de)buffs, crowd control and utility, and healing. Not as good at any as a Wizard or Cleric, but nothing to scoff at either. OK, yeah, their martial ability is pretty poor. But overall, the vanilla Bard can pitch in many roles, and what's more, can make the entire party better at theirs. That's why they IMO make great 5th members in a typical Warrior-Mage-Priest-Thief party.
The vanilla Monk just ... isn't.