They did and they are. You must have missed it, but Charlie and his crew of Calypso developers are not working for Mindark any longer. They work for a company called AR Universe, which is the Planet Partner for Calypso.
The confusion comes from the fact that at least some of them used to work for Mindark and Calypso still enjoys a few benefits above the other Planet Partners. For example, the Calypso developers got the tools to develop instances (beacons) much earlier than other Planet Partners. It's my understanding that they are available now to everyone, but this is the reason why treasure hunting on Arkadia was delayed so long compared to beacons. Confusion also arises from certain AR Universe employees having special access to Mindark (most notably Kim), so that certain changes can be made immediately (mob spawns, loot, etc) that a Planet Partner would need to apply for changes to be approved and wait weeks while they were implemented. I could be wrong but right now, I don't think it's possible for other planets to have invasion events like the one going on now.
So, Mindark IS working to make all planet partners more equal but there's still some way to go. Give them some time, they've had to deal with a lot of fundamental changes over the past year and a half as EU expands hugely each time a new planet is released.
The rebalancing of missions here is just another step in the right direction. They needed to define mission rewards for all planet partners, including Calypso. David Dobson said over on PAF that, at first look, the new guidelines will make it easier for them to develop new missions, because they don't have to go through a lengthy approval process while Mindark decides if their proposed rewards are "balanced". Missions take a long time to develop and faster development of missions can only be a good thing.
And one final note... I think people have been expecting each planet to have its own unique abilities, that the treasure hunting system should only be allowed on Arkadia, for example. I disagree--I think it's better for each planet to have all the same tools, that way all skills are portable and Mindark only has to develop one system. How would you like it if Mindark had to spend 3/4 of their time developing cool systems that could never be used on Calypso? If you look at the seven destinations we have now (4 planets, plus FOMA, CP, and space), they're all very different, and do appeal to very different types of players. Which is a good thing, since EU as a niche game can fill more niches with each new planet.