You've provided three quite unique and very narrow examples.
The first two involve foreign nationals. I don't know, but I doubt CI is a foreign national, and even if MM's question wasn't specific to CI, the Hamdi and Razul cases don't reflect upon the rights of American citizens.
The third involves an American citizen accused of planning a terrorist attack on his homeland.
Yes, one might reasonably argue that holding US citizens indefinately based on a designation as an "enemy combatant" is an infringement upon previously established rights and could open the door to governmental abuse, but the fact is that it didn't. Thus the Padilla case in no way advances the thrust of CI's argument.
Interestingly enough, the Obama Administration is killing American citizens it has decided to brand as "Bad Guys." So far, it has acknowledged killing four in drone attacks. I suppose it's a matter of opinion but I would prefer indefinate detention (with the possibility of legal recourse) than definate death.
I'm not, necessarily, arguing that the four should not have been obliterated by Hell-fire missiles, but if one indefinately detained American citizen means Bush was a tyranical monster, what does four American citizens blown to bits say about Obama?