I find the biggest challenge in implementing real-time emails is getting buy-in from the Website team to add a one-line script to their pages. This is especially an issue when Website technical support is outsourced.
Email Marketers generally like this automation. They need to design a few emails, which is not a problem for them as it's their day job. And they look very good when e.g. cart+browse abandonment emails significantly increase sales.
But Web Marketers are not so sure. There's no upside for them from these extra email-derived sales, they have to install an unknown script on their server, and people shout at them if they accidentally delete the script later.
It's not that the people in charge of the Website are anti-email, but that they are incentivized to meet *their* targets, not those of the email marketers next door who want automated emails.
The best way forward is to ensure that all marketers gain - web and email - by bringing personalization to the Website as well, with multi-channel marketing: automated website messaging and product recommendations, not just automated emails.
Which is exactly what we've done. OK, maybe not complete World Peace, but we had to start somewhere!