1. They're still lacking some major features imho (ability to sell in multiple currencies, can't put tracking JS on checkout pages, access to payout reports for bookkeeper, got lots more)
2. They do terrible product marketing - no email about newly launched features. In an extreme case, they launched a feature that sent emails to customers when their order was out for delivery, delivered, etc. Problem is that I was already using an app for that, so when they launched the feature and enabled it by default without letting me know, customers got two emails telling them their order was out for delivery, delivered, etc. It was a terrible customer experience (for us and for our customers) and I can't imagine how that decision was made. ("Hey, want to enable this feature that sends more emails to our customers' customers without announcing it? Yeah? Great!")
The example you give was extremely frustrating though (wasn't on Plus at the time).
Holy shit, that sounds awful. How do you perform conversion optimization if you can't do tracking on checkout pages?
They try to make it slightly harder to write a store that steals credit cards.. not a terrible thing..
If this is possible it's another example of poor product marketing: I've asked for this feature multiple times via email and forums over the last 6 years, and I hear about it from HN? That's a broken experience for a customer who's paid them approaching 5 figures.
2) No multiple currency support.
3) 100 variant limit per product (I've used a couple different ways around this in different stores, but none of them ideal).
Apps mitigate many of the other missing features and annoyances, but sometimes having to rely on apps is a tough pill to swallow (like needing to use Power Tools just to create smart collections with any kind of advanced rule set.)