Modern concepts, algorithms, and constructions that a designer might not have at their disposal if they rely on Menezes:
* Elliptic curve cryptography, which is supplanting RSA (and Rabin) and conventional DH, both of which are looking increasingly sketchy in 2013.
* Secure RSA padding for encryption (OAEP) and signatures (PSS), or, really, any discussions of the problems that motivate those formats --- Menezes does point out that you don't want to use low-public-exponent RSA with repeated messages, but a modern take on RSA would say that you don't ever want to send repeated messages at all.
* Counter mode, which is presented briefly as a small tweak to OFB mode with no description of its pitfalls; CTR is the second-most popular mode used today and increasingly the first choice of new systems.
* Modern bulk encryption --- XEX, XTS, &c.
* Encrypt-then-MAC (Menezes presents the opposite); in fact, modern crypto is at pains to ensure that encryption and integrity are co-specified and interoperate safely; a designer could be forgiven for reading Menezes and not including explicit integrity checks at all.
* The authenticated encryption modes CCM, GCM, EAX, and OCB.
* Modern CSPRNGs, including entropy collection and management and handling the cold-start problem.
* Any discussion of side channel attacks (in fact, Menezes predates Vaudenay and Bleichenbachers block cipher and RSA [respectively] error side channels so doesn't even discuss padding oracles).
It's not true that robust cryptography appreciates maturity. The ~twenty years since Menezes wrote HOAC haven't just been spent inventing whizz-bang new toys, but also in finding new ways to break the old toys. You're not always OK if you eschew the new stuff for the "mature" stuff; some of the mature tools are perilous to work with now.
That's an annoying thing about working with crypto (and a fun thing about breaking it) --- designers have to know what parts of the literature they need to adopt, like safe RSA padding schemes, and what parts they need to hold off on, like homomorphic encryption.
For what it's worth: I like Menezes a lot as a resource for practicing attacks. Menezes also does a much better job on theory than even _Practical Cryptography_ (which is a great book, and probably the only crypto book most people should own). It's a good book. Just be careful working from it.
(I'm not trying to call you out; I just think this is a fun thing to talk about.)