Uber you seem to be confused. AVR or PIC you can only sample the externally driven timer during a system clock boundary. But on a PIC the timer itself is asynchronous. It's limited only by it's analog bandwidth and the driven signal, which can be WAY past system clock speeds. The AVRs externally driven timer is synchronized to the system clock, Nyquist kicks in real fast, if you try to sample a signal more than 1/4 the system clock of an AVR you're going to get aliasing effects that will mirror harmonic frequencies.
Either way really if you want a truly high speed frequency counter with PIC or PIC you just use an AVR or a PIC and you pick a good external counter and just use the PIC or AVR to sample it, they're both limited on sampling to system clock ticks anyways, and you can get massively higher frequencies with an external counter.