I ordered got both of these the Season 1 & the Crystal Empire DVDs. Season 1 features all the episodes from the first season plus several audio commentaries. The Crystal Empire features the Season 3 two parter plus 3 episodes Sonic Rainbow, Luna Eclipsed and It's About Time which is spread across season but all are great standalone epsidoes.
I've watched all of the Crystal Empire DVD and am working my way througb Season 1 again in DVD form. The audio commentaries are interesting as well.
I'm guessing Hasbro is playing it cautious by seeing how well it sells. Putting it in shops is a more expensive distribution method than simply going via Amazon. If it sells well on Amazon then it may go into shops as well.
I also want to see if they will ever put anything interesting in the next season. Like I would like to see Twilight and her friends make first contact with sea ponies and discover their lost city in the ocean. Similar in a way how they made their first contact this season with the crystal ponies and discovered their lost city in the arctic. Or what about if they ever introduce a centaur pony as well? I think that would be interesting.
Who knows perhaps the fourth season will see the introduction of the sea ponies once more. They have generated a good amount of fan art including sea pony Lyra.