Why take away regular queues at 90?

There are no level 90 regular dungeons.

The Mists of Pandaria heroic dungeons are easier than the Cataclysm heroic dungeons.* Once we made that decision, we thought that having two versions of the level 90 dungeons (normal and heroic) didn't make sense because they would be very similar in difficulty and offer similar loot. We thought about calling them something besides "heroic," since heroic tends to mean hard to a lot of players, but we also needed to call them something, because some dungeons like Temple of the Jade Serpent have a lower-level and a level 90 version. We thought about calling them "level 90 versions" but figured "heroic" required less explanation. (We also could have dispensed with lower level dungeons, or made lower level versions of the level 90 dungeons, but we felt like both solutions were just to make the nomenclature of "heroic" more clear, which seemed like bad reasons.)

TLDR: Some Mists of Pandaria dungeons have lower level and level 90 versions. Others just have level 90 versions. In both cases, the level 90 versions are called "heroic."

* - If you like very difficult dungeons, Challenge Modes are targeted at you.

But what about queuing for the lower level version at 90? I should be able to join a group of friends of lower levels and have the queue work, like it did in Wrath.

If the leader of the group meets the requirements (meaning is below level 90 in this case), I believe they can still queue you, especially if your group is completely premade. I'd have to check this though. We went back and forth on it. In any case, you can always just show up at the entrance to the dungeon the old-fashioned way and zone in.

In general, we don't want players using Dungeon Finder to queue for lower level content that is much too easy for them because then players who want to run the content at the appropriate level are faced with overpowered players who trivialize the experience, or pull aggro off a lower level tank, etc. We have no problem with you running lower level dungeons, provided other players aren't adversely affected.

Are Challenge mode dungeons going to offer more than just speed runs and a flat ilvl? I love the idea but I hopes it's more than just racing against a clock in an easy dungeon in the gear it's meant to be ran in.

At the Bronze level, you'll do good to just complete the dungeon in a reasonable amount of time, but you'll probably need to take it slow and stop and plan. It isn't just a test of who has the fastest movement speed. At the Gold level, you'll need to up your game even more and play smart as well as quick, taking risks where appropriate. The Bronze level is more like Heroic Arcatraz, Shadow Labyrinth or Shattered Halls when they were new. Gold level is more like a Zul Aman bear run when you didn't overgear the content.

That's the intent anyway. Nobody outside these walls has seen them yet so you'll have to let us know how they feel.

Are they actually tuned harder or is it the ilevel lock on them that is suppose to make them hard?

They are tuned harder. There are even some additional pulls and mechanics when necessary.