Ok, I see what you mean.
how about this:

#!/usr/bin/perl
use v5.10.1;
use strict;
use warnings;

use Getopt::Long;

my (@a, @b);
my %options = (
                 'a' => \@a,
                 'b' => \@b,
               );

GetOptions (
             'a=s{2}' => \@a,
             'b=s{2}' => \@b,
           );

say "$options{'a'}->[0], $options{'a'}->[1]";
say "$options{'b'}->[0], $options['b'}->[1]";
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the only problem I have with this is defining parameters for %options before building %options with GetOptions
If for instance I needed to have multiple pairs perl flag, i.e.:

$./program -a a1_1 a1_2 -a a2_1 a2_2 -a a3_1 a3_2
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