Why is 3000 psi the most common hydraulic pressure used in commercial aircraft?
The linked article directly answers the question


  "Above 3000 psi, using aluminum as a pressure vessel becomes risky," says Galloway. "5000 psi systems almost exclusively rely on steel or titanium. To minimize stresses, the sizes of passages can be reduced. Computational fluid dynamics is also used to minimize pressure drop in critical areas."


3000 PSI was the best you could get with technology in the 1950s, when standardization occurred. Without economical titanium tubing and reservoirs, using steel would incur a weight tradeoff that doesn't make sense. 

The A380 was a trigger to the development of 5000 PSI civilian systems because of both the high demands and the long run distances, both due to the size of the plane. I read somewhere that they took a look at the military 5000 PSI systems and realized it would never stand up to commercial use, so little technology was carried over.

Every new design large transport from the A380 onwards (787, A350) is 5000 PSI.