Your history is incomplete.
You're aware there were hordes of Apple II clones, right? I started my computing life on a Franklin ACE 1000 - a superior clone of the Apple II. After it died, I got another Apple II clone (A "Laser 128" as I recall). There were Apple clones for over ten years with the Apple II, and several more years with the Macintosh.
Apple II clones died for two reasons: The Apple II was a very old architecture, only capable of 64k of memory. Also, most of the cloners illegally copied Apple's BIOS. Even then, Apple vs. Franklin was in 1987 - ten years after the Apple II was released.
IBM did sue clone makers into oblivion. In fact, after Apple vs. Franklin, IBM sued a number of early cloners out of existence for the because they also illegally copied from IBM's BIOS.
The difference is that nobody saw the point in writing a clean-room Apple II ROM in 1987. The world had moved beyond 64k, and there was no point in denying reality. Even Apple was pounding nails in the Apple II's coffin.
In contrast, Phoenix and AMI both had clean-room IBM BIOS clones written in 1984 and '85 - years before Apple vs. Franklin. IBM couldn't touch Phoenix or AMI.
So IBM tried to destroy cloners by creating the backwards (but not forwards) compatible PS/2, complete with their backwards (but not forwards) compatible OS/2.
In the end, it came down to price: A clone was more capable than IBM's PS/2 disaster, and had a cost far less than the PS/2 or a Macintosh.
IBM tried its best to kill the PC clone. The difference is that unlike the Apple II, the PC clone could handily beat the PS/2 that was supposed to replace it.
Never forget: The PC clone didn't just beat the Apple Mac - it beat IBM's replacement for the PC as well.
And it did so for the same reason Timex has far more market share than Rolex or Tag Heuer: It does the same job for a lot less money.