1) It require code changes ... could be done when you're starting from scratch but nearly impossible for existing projects with really large code base. Moreover most PHP frameworks already provide similar functionality with deeper integration and better reporting.
2) This is the real dealbraker: having to add code manually means that eaither you go crazy and add profiling everywhere or it wont really help you because you'll add profiling only in the most obvious slowdown point and you'll discover what you already knew. But you'll probably loose hidden bottleneck in place you could not easily guess.