/.../&&print||splice@_,0,2for@_    #31 chars
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My [update: broken] entry:

(/^..$/...$_)||print for@Array # 30 chars, with named array
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---

Caution: Contents may have been coded under pressure.

my @Array  = ('AAA','BB','CCCC','DD','EEEEE','FFF','GGGG');
(/^..$/...$_)||print for@Array;
__END__
AAAFFFGGGG
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But according to the OP, it should not exclude the 'EEEEE'. Your solution excludes the entry that has 2 characters, and the next one (or rather, until the next one that is true). The result of your program will change if you replace 'CCCC' with '0', or 'DD' with 'DDD'.

Please, recheck your code - it is skipping more elements.

Another 31 chars:

print split' ..( \S+){3}',"@_"
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Problems:
1. The array is called @Array, not @_.
2. Modifying an array you're looping over isn't well defined.
3. It will attempt to skip over 2 elements for all strings less than 3 characters, not just strings of exactly 2 characters.

my @Array   = ('AAA','BB','CCCC','DD','EEEEE','FFF','GGGG');
my @Skipped = split' ..( \S+){3}',"@Array";

print "@Skipped"

__END__

STDOUT: AAA  EEEEE  FFF GGGG

Right?
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use strict;
use warnings;

my $num_of_skip = 2;
my $skip        = 0;

my @Array   = ('AAA','BB','CCCC','DD','EEEEE','FFF','GGGG');
my @Skipped = grep {$skip-- if $skip; $skip = $num_of_skip + 1 if !$sk
+ip and length($_) == 2; !$skip; } @Array;

print "original: @Array\n";
print "wanted:   AAA EEEEE FFF GGGG\n";
print "output:   @Skipped\n";
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grep{$skip--if$skip;$skip=3if!$skip&&length($_)==2;!$skip;}@_ #61 char
+s
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