You can keep a flag to say that an element should be skipped. It appears that you also want to skip the triggering element, and that a skipped length-two element does not trigger. Those properties will be controlled by the order of test and flag manipulations.

#! /usr/bin/perl -w
use strict;

my @Array = ('AAA','BB','CCCC','DD','EEEEE','FFF','GGGG');
my $num_of_skip =2;
my $skipping = 0;

for (@Array) {
    $skipping++, next
        if $skipping and not $skipping > $num_of_skip;
    $skipping++, next if 2 == length;
    print $_, $/;
    $skipping = 0;
}
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