@tanonev: Remember that nothing in the rules (current or proposed) causes anyone to forget that the invisible person is around. Consider this:I see a rogue duck behind a corner/behind a bush/in the shadows/whatever. I know they're there, but I can't see them. I approach cautiously, but because I can't see them (despite knowing they're there), I can't prepare to properly defend myself - I'm flat-footed against them. Not because they were 100% imperceptible, but because I couldn't see/perceive them clearly enough to keep an eye on their movements and defend myself as properly as I could if we were dueling on equal ground. Naturally, knowing that the rogue is (probably) waiting for me behind the foliage, I could prepare myself (ready an action to go into total defense, etc).
That's why we don't need rules for "marking" or "tracking" a stealth'd character - you already can. The stealth-granted invisibility (or whatever the final effect is) doesn't represent totally forgetting where he is, it represents not being able to track his movements closely or precisely enough to engage him "properly".
The logic that I can't prepare to properly defend myself against something that I can't see applies to line of sight, not Stealth. Consider the flip side of how the rules currently (and will continue to) work: If I'm a guard, and I beat the Stealth check of a low-level rogue on the opposite side of a 20-foot-square wall (e.g., he accidentally drops a potion that shatters), then while I clearly can't actually SEE the rogue, I can still "defend properly" (keep my dexterity bonus) against whatever the rogue does when he pops out from behind the wall (including, apparently, using a brilliant energy weapon and x-ray goggles to attack me THROUGH the wall). And if beating the rogue's Stealth so that I know that the rogue is there behind the wall is sufficient to allow me to keep me dexterity bonus against being stabbed through the wall, then me knowing that the rogue is in a particular shadow should be sufficient to allow me to keep my dexterity bonus against being stabbed from the shadow.
Actually, it would be nice to clarify: What exactly does it mean to beat someone's Stealth check, especially if you don't have line of sight? Similarly, what does it mean to fail to beat someone's Stealth check? A lot of the language suggests that a lack of line of sight = automatic Stealth (see, as a random example, what happens if you have faerie fire on you and you head well out of sight--unless faerie fire was also modified to make you sound like a firecracker).
Incidentally, depending on which Stealth implementation you choose, readying an action to go into total defense doesn't do anything, since total defense provides a dodge bonus to AC, which is negated whenever you are denied dexterity. And since a readied action completes before the trigger action completes, if Stealth doesn't break until after the first attack, the dodge bonus will be wasted on the most important attack. In fact, if Stealth doesn't break until after the first attack, it doesn't matter what you ready, since you can't meet the trigger condition for a readied action until after that attack, because a trigger has to be observable (while the rules don't explicitly state that, allowing characters to ready actions on unobservable triggers is pretty clearly abusable and unintended).