Doom 3 level structure...

Which would be better? Classic doom map1 then 2 then 3, Hexen like hubs, or something else?

Hexen-like hubs would be the least they'd do. I'd probably go for the "something else" part, although if do make any hubs as hard as the egyptian one I'll hang them all.

System Shock 2, go wherever you want. It shouldn't be really necessary for the game's progression, but it's always good to go back a few steps if you forgot a gun or something like that.

Ok, here we go... I doubt that the 'one map after another' style will make an appearance in Doom 3. It is usually present in 'mission based' games whichare less... imersive than it seems the new Doom will be. At the same time, I don't think it will give you the ability to roam that was present in SS2. The reason SS2 was able to do this was because of the relatively compact size of the ship you were in. A base on Mars (or either of it's moons in the event of a re-make) has little vertical development and spreads out more horizontally. Though it is possible to allow you to revisit any area you wish, it would generally take a long time to get most places.

The way around this: The center of the base is the hub and you can walk to the buildings whenever you wish.

The problem with this: You lose a lot in the story development. It also adds exploration (to some extent) into the picture. As with any large central HUB, the levels cannot stray too far away, and if they do they must eventually loop back around to the HUB. It doesn't sit very well with the idea of teleporters either.

My opinion: Level progressions should and (and for purposes of effort) will probably be in a linear fashion. This doesn't mean that the levels are linear, just that there is a clear progression from level 1 to level 2. I am not opposed to a few deviations from this, and a HUB or two are fine, but I don't want the game focussing on them. It detracts from the feel. Linear level progression does not mean that you can't go back into previous levels. A few threads down sombody mentioned having the levels change the longer you play (though this is really increases level designing/building time). Even if the levels don't change, going back could add to the realism of the game (instead of all your objectives being linear, you may have to go back to where a certain part of the base was).

By no means should this continue throughout the whole game. Perhaps some 'disaster' could close the path behind you. This would cause you to need to find another way to get back to a needed area, or to simply force you to focus on moving foward.

A few of the comments made about the game lead me to believe that Doom 3 will be more story based. If this is the case then, whatever the level set up, the game needs to be designed in a way that brings out the story. The story makes the levels, not the other way around.

I hate hubs. I always get lost in them :(