The explanation I heard was that theme encounter powers are not as strong as normal class encounter powers; they're balanced more like at-will powers in power level. They don't net you much extra power, just give you an extra option once per encounter.
This would be how I would design them for core D&D, but Dark Sun powers are definitely stronger than at-wills, as has been pointed out by others.
One of the drawbacks I apply (I guess as a houserule) is that if you choose a theme, you cannot gain a background bonus per the Player's Handbook 2. Your skills are less impressive, unless your theme says otherwise.
When they make themes for core D&D, I can see one of three things happening:
1) The feature powers are on par with at-wills, either actually being at-will or being encounter powers that are only as powerful as at-wills. This gives a character more options in a battle, but not necessarily increasing their statistical power. Themes from Dark Sun would be disallowed in a core D&D game.
2) They continue making themes in the same way, but introduce some drawback mechanic that makes it balanced. When playing in Dark Sun, you don't apply this drawback mechanic to compensate for the harsher environment. This would be good, because players could use Dark Sun themes but adapt them for a homebrew game world that's not as harsh as Athas.
3) It's a power creep; deal with it. The monsters got stronger, but now so have the characters. The general themes are the same as the Dark Sun ones with no new drawbacks.
I prefer number 2, but I wouldn't mind number 1. I would be annoyed if they are going with number 3, but I would just sigh, go along with it, and continue having fun.
PS: Maybe as a houserule, you could just increase the price of trail rations to 5 gp per 1 day worth of food and water, like a survival day in Dark Sun.