MAD: You need Wis for AC, Dex for AC, Con for HP, Str for to-hit and AB. You also can't dump Int since skills are pretty important.
Low AC: You can't wear armor, meaning that your Wis needs to be higher than the Armor bonus the Rogue is getting. Generally, you fall behind on AC. MAD excabrates this.
Low AB: Flurry of Blows costs at low levels, and the partial BAB doesn't help. By high levels, Fighters are Power Attacking for 20 and still hitting, so the fact that you can, too, isn't helpful. MAD excabrates this.
Low damage: You have to stack size increases(not easy) to get your fists up to dealing good damage, and you still end up not great. MAD excabrates this.
Wierd/useless abilities: Tongue of the Sun and Moon? Really? Are you really in so many situations where you need to speak Treant and the casters can't cast Tongues? Most of their abilities fall into similar problems by either replicating low-level spells or being too situational(or both), with the Capstone being nearly as much of a nerf as a benefit. SR is useless, too, blocking allied combat buffs and not helping with the BBEG casters or certain low-level deadly spells.
Limited abilities: A lot of their abilities only happen once/day, including the Fort SoD that is once/week. Speed boosts that don't stack with(and are inferior to for half of the levels) the most common spell to boost speed. Just not useful.
Poor synergy: Lots of movement-based abilities and skills, then a major class feature that requires a full-attack. All of their attacks target either Fort or AC, which are generally either both low or both high. The special combat actions are always either Str-checks(which MAD wrecks), AB checks(ruined for obvious reasons), or penalize light weapons and boost THF, meaning the Monk is poor at them.
Low skill points: Really, you expected me to put something here? Fine, MAD excabrates this.
Poor proficiencies: You're limited to using 'special Monk weapons', most of which have poor base damage and weak special abilities. Effective PA is pretty much closed off to you, and most of the weapons are Light, meaning special combat actions are harder. You also have no reach weapons at all, meaning that AoO(the normal method for dex-focused special combat action-based fighters) is sharply limited.
Unarmed wakness: Unarmed strikes cannot be enchanted, meaning you have no way to overcome DR/Silver or similar, and no way to strike incorporeal creatures at all. Yes, you can buy magic Kamas or something, but then why aren't you playing a Fighter and using something good?
Not saying they don't have uses, or that a Monk can't be optimized to be great, just that generally other classes are a better fit most times.