I'm skeptical. If you are going to say that games get it right, I would like to hear examples. Dragon Age: Origins has manual stat allocation, and it is just one part of how that game is a complete mechanical disaster full of bad design choices.
A lot of Western RPGs are heavily influenced by tabletop RPGs, most notably Dungeons & Dragons. It is Dungeons & Dragons that invented and popularized the idea of stats and the importance of stat allocation. However, D&D's basic mechanical framework is built on very a very shaky foundation that people have been increasingly criticizing over recent years. It's use of stats as the foundation of character abilities are fundamentally at odds with its class/level system.
Here are common pitfalls that stat-based games have fallen into, based on the mold of D&D:
1) Unequal value of stats.
If one stat is more powerful than another, then having the player be able to put a point in either one for the same cost won't work. However, it isn't easy to have a system where every stat has equal value. Furthermore, there are a lot of game systems that barely even try (the difference in value between Dexterity and Constitution in many editions of D&D, for example). Final Fantasy 6 has something resembling manual stat allocation via its Magicite level bonuses. The problem is that it isn't at all obvious which stats do what. For example, Vigor mostly effects how much hp damage/healing poison and regen effects do. Magic Power boosts everything from the obvious (Magic spells) to the nonsensical (Sabin's Blitz attacks). The game presents these as equal options, but one is vastly better than the other, almost to the point where building up Vigor at all is a complete waste.
2) Multiple Ability Dependancy (MAD)
This is something that comes up in class design, where different classes require more stats to be high than other classes. For example, in Dragon Age Origins, a sword and shield using Warrior need Strength and Dexterity to unlock their talents, Constitution to actually survive hits, and Willpower to afford actually using their skills. Meanwhile, a Mage can get by via mostly just pumping Intelligence and Willpower. Both characters get the same number of ability points from a level, but one has to spread them out among twice the number of stats.
3) Making players choose between being good in combat and being able to do non-combat stuff
You thankfully see this less often than other problems, but it still happens a fair bit in WRPGs. This is where a game makes the player choose between putting their stats in their combat skills, or putting them into stuff like being better at conversation options or opening treasure chests. However, no matter which way you look at it, being better at conversation options is never equivalent to being better at combat. They are so fundamentally different that you can't balance the two.
4) Buying stats you can't use.
In a game with a class system, why would a Fighter put points into Intelligence, if Intelligence is only used to determine magic power? It would give zero benefit. The problem is that a lot of systems don't prevent this from happening. In some cases like the example I gave, it might be obvious. In other cases, it is less so.
These kinds of problems are big enough that even some D&D fans I have seen want to get rid of stats from the game. A lot of modern tabletop RPGs have replaced stats as a whole with alternative systems for describing characters. So I am not convinced that manual stat allocation works very well. It has a lot of problems built into it. There are games that do it well by balancing stats very carefully and making stat allocation into the basis of the whole game, such as Demon's Souls. But that takes a very delicate touch, and doesn't work if you try to tie stats in to non-combat options like a lot of D&D-inspired WRPGs.
EDIT: It is worth pointing out that automatic stat allocation is not the same thing as having no builds or character customization. I just means that the emphasis is on systems such as classes, ability choices, equipment choices, and so forth. I would say that those things are not only more intuitive to work with, but have a greater ability to allow for a variety of character builds than pure stat allocation systems.