As an Ingresser myself, I'd say there were two big sources of issues vs. your typical Ingress anomaly, and one that would happen in Ingress if it was a bit closer in popularity.
First off, they had everything in one place. For those who haven't played Ingress to that point, anomalies in Ingress usually take place with a primary and two secondary locations in, roughly, Asia, the Western Hemisphere, and Europe. This means that people aren't usually traveling from far away (which probably would increase overall participation) but also that each site's numbers are lower. I figure overall anomaly attendance on a given anomaly weekend might well rival that of this event -- but they're spread out in geography and time.
The second aspect is that Ingress has much more encouragement in-game of local organization. I understand quite well why Pokemon Go lacks in-game chat, but it saps local organization. Locals play an important, perhaps critical, role in Ingress event organization, and provide Niantic with free boots on the ground to figure things out. I know there is some local organization going on in Pokemon Go, but it's forced to be based on random encounters, and folks are still unsure whether to organize on team lines or just geographically. (With the current setup, I'd say geographically -- if there's anything to be learned from Ingress, it's to tamp down factionalism.)
The last thing, the one that I think would hurt Ingress equally? It seems there wasn't a limit on ticket sales. In Ingress some special extra-value packs that get you extra tchotchkes both virtual and physical exist, but the base 'free' ticket is unlimited. Similarly, here. They probably wanted to avoid any chance of scalping or the like, but imagine if they limited it to, say, a quarter the attendance?