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I mean, you could force the stopwatch. It's only a one time use. If they're rushing Zhonyas, then obviously you can't kill them, but it probably means you've delayed morello's. Zed is an extremely safe assassin. Don't really see what the problem is here.
The problem is that I have to win lane pre 6 if I want any possibility of snowballing the lane vs Stopwatch. This means that basically I am at the mercy of my opposing laner's stupidity as Zed gets shit on by most mids pre 6.
Being a safe assassin is nice but not entirely true as Zed's safety is also his trading ability that's on a 20 second cooldown. Zed isn't Kat/Akali who can get out of lane 0/0 or 0/5 and still get to impact the game, he needs to get an advtange to be impactful (which is why keeping up the gold and exp by splitting bot while botlane arams mid is essential).
If then Zed managed to win lane/snowball, there's ADC's running around with Stopwatches and/or GA which also happens to be a perfectly viable item for them, making them virtually unkillable in the lategame. Zed's drastic drop in WR% after the 20 minute mark supports this. (Obviously)
TLDR: Zed depends on getting an advantage early but Stopwatch and origami towers that punish roaming make it (too) difficult.