So here's the deal. Let me explain this to you peeps who weren't around for 1st and 2nd edition or have poor memories.
There was a time when we actually had to roll our hit points at 1st level. That sucked. (As an aside, 1st-level hp still sucks in 3.5. A lucky hit from an orc can take down a 1st-level dwarven fighter. And with the MM giving them falchions those lucky hits happen more often than they probably should. Anyway...) If you rolled up a 1st-level fighter and got some awesome stats, say a 18/57 Str, 16 Con, 17 Dex, you were feeling invincible, then that d10 roll came around and stared you in the face, said "I am going to do horrible things with your life" and turned up a 1. Suddenly you were stuck with a 1st-level FIGHTER with 3 hp.
Now the designers for 3e came from this perspective. Most of them had played AD&D for years and looked at that 1st-level hp probably and realized it was a design flaw. They came up with two solutions for it, but this is a clear case of the right hand not knowing what the left hand was doing because one fix negated the need for (and in fact the usefulness of) the other. One fix was to maximize 1st-level hp, a house rule many DMs had been using for years and favored by many players; a similar house rule was to allow minimum 1/2 HD regardless of your roll for 1st-level. Another fix was the Toughness feat. Now the formative idea for feats was based partly on some player options that had existed in AD&D; Power Attack is one example. Another part of the idea was that feats could allow players to choose where to focus their modifiers and bonuses. Feats like Toughness, Improved Initiative, Alertness, Spell Focus, Weapon Focus, all of these were designed to give players control over these things. At the time, still coming from the perspective of having to roll for 1st-level hp and not knowing which "fixes" would make it into the final draft, having Toughness around seemed like a great option. It would double the hp of that poor fighter who seemed so awesome at the ability score rolling phase but crapped out in the hp roll phase and give him a chance of actually surviving to higher levels where he might take advantage of those nice scores. And even if it didn't turn out to be necessary to fix the "roll for hp at 1st-level" problem, it would still help squishy casters survive low-levels right?
Well it turns out the Toughness feat was one of those things that sounded great from an AD&D perspective (tell me an AD&D character who wouldn't want 3 more hp) but wasn't after 3e was done. They had a chance to fix it when 3.5 came around but didn't.
I've had a number of fixes for it over the years, but the best is to simply treat the Improved Toughness feat as a "patch" to Toughness. You can even let players take Improved Toughness as many times as they want. It won't break your game.
