Actually, it turned out that scrypt was not as good as initially advertised under all conditions.
Scrypt was designed to support the specific case of password-based key derivation for full harddisk encryption. Basically, you type your password when the machine boots up (or awakes from hibernation). This is a context where the following apply:
The password processing time can take several seconds, since it is part of a boot-up procedure that will take a lot more time; under such conditions, user's patience is such that 5 seconds of dedicated time is not an unreasonable figure.
While the password is processed, nothing else happens on the machine, so the full CPU can be used for the task, and also the full RAM (so up to gigabytes).
In that context, scrypt totally rules. However, a busy authentication server, e.g. for an active Web server, can be a different beast. In particular, you will probably want to make the per-password CPU cost much lower, not only because there may be several users to handle simultaneously and concurrently with other tasks, but also because the more expensive password hashing is, the more vulnerable you become to basic denial-of-service attacks. For a busy server, a computing time down to 1 millisecond or so would be a more plausible value than the "5 seconds" alluded to above.
When scrypt must run fast, it cannot use as much RAM. In fact, at 1 ms CPU time, it uses so little RAM that GPU-based optimizations become to be worth the effort. In Litecoin, scrypt is used with 128 kBytes of RAM, and GPU implementations can be about 10x faster than CPU implementations (for the same hardware/operating cost), which is technically a function failure. One of the main points of a password hashing function is that attackers with GPU should not gain an advantage over defenders who use "normal" CPU. For fast password-hashing, bcrypt thus turns out to be more secure than scrypt. While scrypt is better than bcrypt when used for what it was designed for.
A further issue with scrypt is that it allows a time-memory trade-off: with more RAM, you can save on CPU, and vice-versa. This kind of flexibility gives some leverage to attackers who try to optimize their effort.
You may want to consult this presentation for some explanations and pointers to further information. The raw conclusion is that while scrypt is reasonably good for what it does, it cannot be said to be a drop-in improvement over bcrypt.
(As a side note, take care that use of a password-hashing function in cryptocurrencies is not the same context as use for protecting passwords in an authentication server. In an authentication server, there is an asymmetrical race between attacker and defender, because the defender uses generic hardware while the attacker can buy special-purpose dedicated hardware. In a cryptocurrency, miners compete against each other and they all buy the same GPU or ASIC anyway, so the 10x GPU speed-up in Litecoin is not a problem for Litecoin; it would be a problem, on the other hand, for an authentication server, where the defender must work with whatever PC he can get from his hosting provider.)
Such things prompted cryptographers to look for better password-hashing functions, and they did so with the usual arrangement: an open competition(*). This resulted in the Password Hashing Competition. The process took a few years and resulted in the choice of a "winner" called Argon2 (along with four other schemes with "special recognition").
The current situation is not ideal in that we now have the choice between:
the old bcrypt, that is reasonably good except against the very serious attackers who think big and use FPGA;
the newer scrypt, which is better than bcrypt in some contexts, but worse in others, and has some extra drawbacks;
the brand-new Argon2, who sustained some rather heavy scrutiny, but only for a limited amount of time, and thus cannot be universally recommended yet.
The bright side here is that the PHC appears to motivate extra research on Argon2, and that is good.
(*) For cryptographers, the most perfect academic process for research is the Thunderdome.