One significant problem with PKG_CHECK_MODULES is that it causes failures where it should not. If a user installs libfoo in /p/a/t/h and invokes a configure script with LDFLAGS=-L/p/a/t/h, the user is justified in expecting the configury to find libfoo. But, the user also must set PKG_CONFIG_PATH so that the configure script can find foo.pc in order for the configury to succeed, and in my opinion that is broken. It would be possible to invoke AC_CHECK_LIB and then only invoke PKG_CHECK_MODULES if the library is not found through the standard mechanism to avoid that problem. Another issue is that it is entirely possible for PKG_CHECK_MODULES to find a .pc file in which the information is inaccurate, causing the build to fail. In that case, it is necessary to invoke AC_CHECK_LIB after PKG_CHECK_MODULES.
In short, to use PKG_CHECK_MODULES correctly, it is necessary to invoke AC_CHECK_LIBS first, then conditionally invoke PKG_CHECK_MODULES, and then invoke AC_CHECK_LIBS again to validate the information found by PKG_CHECK_MODULES. All of this additional work on the part of the maintainer just to make it easier for users to install their libraries in non-standard location is absurd. The user should set up their tool chain to find libraries through the standard mechanisms.
— EDIT —
To clarify, I am not suggesting that a package which uses a library which encourages the use of PKG_CHECK_MODULES should avoid using it in their configury. Rather, I am recommending that libraries not encourage its use and stop distributing .pc files. The problem that is trying to be solved by .pc files is better addressed at a higher level. The autotools are not a package management system, and this is a problem that should be addressed by a package management tool.