That's because the numbering only gets bumped for sufficiently "major" upgrades, typically marked by a redesign. There was the original iPhone, then there was the 3G (which introduced 3G and a new design) and its minor upgrade the 3Gs, then the 4 (which introduced the retina display and a new design) and its upgrade the 4S, then the 5 (which introduced the new aspect ratio).

Or HTC from naming their newest flagship phone the "HTC One".

3 wrongs don't make a right?

Or Sony calling PSOne a modified/updated version of the first Playstation.

That actually was the same thing as a PS1 and they stuck to that convention. The PS2 slim's official name is the PSTwo.

Actually, no, they abandoned that convention. The PS2 slim's official name is the PS2. It just has a different part number.

Yeah, man. Why did this stupid developer call her newest release "Program 2"?! It’s her third release, after all, she already released Program 1.0 and Program 1.1.

To want to call the iPhone 5 iPhone 6 is so insane, I cannot fathom how anyone could come up with this crazy idea.

It would be more like calling it Program 1 after releasing Program and Program Upgrade.

Or nintendo using Wii U for the Wii successor