The existing answer cites the specific issues well, but having come out of playing a Truenamer (and being so offput by the experience that I have even created a rewrite of the class that I use for my own games), I would like to give a look into what the problems feel like.
Low build flexibility
Truenamer is not a class for the faint of heart. Similar to a Monk, getting one to work half-decently requires an incredible amount of effort and optimization. Unless you're happy doing nothing but making knowledge checks, you need to dump an incredible amount of resources into your Truespeak check.
Other casters do not have to think nearly as much about how they build as a Truenamer. A Wizard can pick bad spells, sure, but at least he can cast those spells. A poorly optimized Truenamer has a very high chance of legitimately being unable to contribute at all. That's a far worse fate than an unarmored Cleric who only heals or a divination Wizard who only casts fireball.
As a result of this, Truenamers have a very hard time working outside of a very small niche, even with competent optimization. Planning out a build was really tough, for instance, because so many of my resources were spoken for with trying to keep my Truespeak up. I had to pick a race with an Int boost, I had to take Skill Focus, I had to take Quicken Utterance, I had to shell out gold for a Headband of Intellect and an Amulet of the Silver Tongue, and my multiclassing was heavily restricted.
As a comparison, while other casters certainly have a hard time multiclassing, they can do it a lot more freely than a Truenamer. That's true of other similar-chassis non-Vancian casters, too; I could make a lot more unique builds with a Wilder, a Warlock, or a Psychic Warrior than I could with a Truenamer.
Truenaming is inconsistent
Let's suppose, however, that you're going single-classed Truenamer. You're following the cookie-cutter guide to the build and have Truespeak for days.
You're still inconsistent.
Firstly, you have some additional vulnerabilities that most casters don't have to deal with. Intelligence damage hurts you more than a Wizard, skill check penalties from conditions like Shaken can throw you off, and you're just as useless against Anti-Magic Field as any other caster.
Second, it's incredibly rare that your Truespeak checks are legitimately guranteed. This is a hindrance at all levels of play, since utterances don't seem to be balanced around this. Utterances are, at best, comparable to spells of a similar level. However, those spells can be cast with guranteed effectiveness.
Even if you have a gigantic Truespeak bonus and you are facing an opponent with a reasonably low CR (not always guranteed - some monsters have inflated CRs and are thus disproportionately hard to utter against), you will still have a chance of at least failing when trying to use Quicken Utterance. In a system where casters of every flavor are generally expected to be able to tell the action economy to go sit in a corner, Truenamers can only do so with a certain percent chance. You're like a Wizard who has been forced to wear armor.
Perhaps, in the cold and sterile labs of balance calculations, this seems reasonable. However, it feels awful at the table when your party gets screwed over because you rolled a 1 when trying to utter an Inertia Surge. There's a reason arcane spellcasters don't ever use armor despite the spell failure chances seeming small at first glance.
Utterances are not worth the cost
All of these pains would be worth bearing if the things that a Truenamer could do were at least decent. Unfortunately, that's generally not the case. Certainly not past low levels.
Don't get me wrong - there are legitimately incredible 1st level utterances. Inertia Surge and Universal Aptitude are incredibly powerful abilities for a 1st level character, and they age pretty well into higher levels. There are even a few 2nd level utterances that I got a surprising amount of use out of.
At 3rd level and beyond for the Lexicon of the Evolving Mind, and at almost every level for the other two lexicons, the pickings are very slim. Most utterances are just rehashes of things a Wizard, a Bard, or a Psion could do much earlier. Psychic Warriors and Duskblades can even get a similar or greater amount of utility if built with the same degree of effort as a good Truenamer at mid levels. All of this without a restrictive random chance of failure and a set of convoluted penalties that build up over the day.
Conclusion
Don't get me wrong - the class is usable. There is a beating, working heart of this class that is compelling and fun. It's just very hard to get to past all of the flaws, and the effort required on the part of both the player and DM to do so is significantly more than the effort needed to just use or reflavor another class. Instead of houseruling away the Law of Sequence, the Law of Repetition, and the conflicting bonus types, just play a nerdy Bard whose performances are ancient and indecipherable poetry. Maybe even ask the GM if you can use Intelligence as your casting stat instead of Charisma. You will get something a lot more functional that scratches the exact same itch.
