What aspect of GOP primary rules allowed trump to win nomination?
The main thing was the preponderance of Winner-Take-All primaries, which allowed him to, for example, win 100% of South Carolina's delegates with 33% of the vote and build up a lead which eventually became insurmountable that way.
However, more so than the primary process itself was the pre-primary process in which the Establishment coalesced around Jeb Bush, who then proceeded to flop spectacularly in the election, but yet who was unable to drop out due to his commanding lead in fundraising and endorsements. The murder/suicide of negative campaigning between Bush and Rubio helped him too.
I agree with the first part but the idea that the establishment rallied behind Jeb is a myth. 2016 was a wide open field that left the GOP vulnerable to the rise of an outsider candidate like Trump. This contrasts with 2012 when Romney was the only viable establishment candidate and was able to overcome a divided opposition. Most establishment politicians never endorsed a candidate and the establishment did not rally around any candidate, Jeb or Rubio, as they had in previous years to candidates like Romney and McCain. Bush was merely one of many candidates and getting 10-20% at his best was never a great position for him. The open field was the reason Jeb or other candidates didn't drop out as they all presumed Trump would crash and then they could all have a shot. The establishment nor the establishment vote ever coalesced behind one candidate-the closest they came was at the very end with Ted Cruz(!) and while that gave him his Wisconsin win it was too little too late. A split field was a key factor in helping Trump win, the lack of a frontrunner and not the presence of any flawed one.
http://fivethirtyeight.com/features/jeb-bushs-path-to-defeat-began-a-year-ago/
Don't overestimate the pull of the establishment wing of the party. In 2008, the 'establishment' mostly rallied behind Romney, but he still lost because Moderates rallied behind Mccain. Moderate Republicans should be considered another branch of the party (these are more economically liberal/socially liberal Rs). Most moderates backed Trump, the only other candidate to collect a high percentage of this group was Kasich.
Jeb's path to the nomination was to consolidate these moderates, Trump complicated the dynamic for him. This was furthered by Trump's constant attacks against him while a number of other competitors stayed silent as the article points out. Through wear and tear his numbers began to decline, this series of events repeated whenever Trump attacked a rival.
If the GOP wanted to unite against him they needed a cohesive ideological platform on which to oppose him. You mention Cruz, but yes, they mostly refused to make this argument. Walker and Cruz were the only two candidates that attempted to do this, but they were undercut through the dynamic of Trump's competitors staying silent while they were receiving the brunt of attacks (ironically, Cruz initially participated in this process to the detriment of Walker).
