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It's because of the pure randomness with theese skills. I also had this wtf moments alot this evening. For example:
Node 1: I use skill and get a 45% chance to HQ. Result was I got NO HQ item from the node.
Node 2: I didn't use any skill. I got 4 HQ items out of 5 attempts.
In these moments you indeed think that these skills are just eating your GP and they feel simply useless. And it's nothing new. I remember the random devil from FFXI when something had a chance to drop around 50% and you still didn't get anything after 15 attempts. That's why I only like the skills which yield more items, because it does also mean you'll get more HQ items on standard nodes.
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It's not a theory, it's fact.
There's a soft cap of 15% that never increases without either abilities or the +5% node. So, anyone who's bought a tier IV perception materia has basically wasted their money.
That is bad design on SE's part.