Well, maybe that was because they had a lot more money to throw at R&D? Not saying either way, but it looks like this was the opportunity that really pushed Intel into the big league. To their credit, they used it wisely and kept making better chips.
Intel's chips continued to advance after those designed by the AIM Alliance (Apple IBM Motorola) hit their ceiling, so I'm not sure it was just R&D budget.
I was impressed by the performance of the PowerPC 970 but much sooner than expected, Intel's (and AMD's) lineup made it irrelevant.
It's more like Intel had a CEO that understood what it took to win in the CPU business and Motorola ended up with a CEO that printed out his email and banned Macs from the company when they were one of the few licensees making Apple Mac clones and Apple was one of their biggest buyers of CPUs.
I would attribute that more to Intel's revenue than anything special about the company though.
As others have noted, Intel was in cash and drove on top of that mostly. Not to belittle Intel though. Motorola would do well, as evidenced by 88k and later PowerPC with Apple and IBM... but at that point in time it was already too little too late.
They didn't really trounce all the RISC vendors until AMD showed them the way with x64. They wasted a lot of time on Itanium.