Akali's stealth suggestion
Personally, I think the true stealth should stay.
However, the problem would still remain that it has too little counter-play and by itself is hard to mess up, especially as a defensive option.
Therefore my suggestion is simple; It should require more skill to maximize its use, especially under tower. Its way too easy to use compared to even making an attempt at playing around it.
For example:
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You could make it so proccing your passive is what extends the duration and not just walking in and out.
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There could be conditions, which if not met reduce its effectiveness. One instance of this that's in line with the first example is; if you don't proc the passive in maybe two seconds of deploying the shroud the duration gets a big cut akin to Kayn's wall walk. Other conditions for that duration cut could be taking a certain amount of damage (whether during stealth or otherwise or both) or staying within the shroud too long.
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There could be a limit on the true stealth. This could be achieved by something as easy as only having one charge, even if just in situations under tower. You could also have an ammo system like
with his rockets or something akin to 
where after using the ability you have a certain amount of charges (or duration) of true stealth.
Another case could be you start with only one charge on cast and you can gain charges with certain successful actions. These actions could be; proccing passive, landing a high energy 'q', landing the 'e' on shroud, hitting more than one champion with either proc of your ult.