well you also need to consider that each DVD and blu-ray volume release for the first 2 seasons only contain 2 episodes per disc, while each release for S3 contains more episodes per disc; volumes 1 & 2 for S3 contains 4 episodes per disc, while vol.3 has 5 episodes per disc, so if you calculate the amount of money you need to pay for 2 eps per disc compared to 4/5 eps per disc, S3 is actually cheaper because you get more eps for less. Take the regular edition DVDs for example, you need to pay 3500 yen for just 2 eps of S1 & S2, but you can get 4 eps of S3 for 5800 yen; that's

1200 yen cheaper per volume than S1 & S2.

For the limited edition blu-rays releases, most of the volumes for S1 & S2 cost 6500 yen each (only vol. 1 & 13 cost 7500 yen), including all the bonus charms and booklets, but again you only get just 2 eps per disc/volume. While the LE blu-rays for S3 cost 8800 yen for vol. 1 & 2 (4 eps + bonus booklet), and 9800 yen for vol. 3 (5 eps + booklet); that's a whopping

4200 yen & 3200 yen cheaper respectively than S1 & S2. Even though the LE blu-rays for S1 & S2 also include the charms which S3 does not, but would you really rather pay an extra 3200/4200 yen per volume just for a bonus small charm?