First, I would like to say that I’ve only had my WP Engine experience because I’m working on somebody else’s website, and that website is hosted at WP Engine. There may be some great advantages to using WP Engine, but I’m not in love.
I’ve already mentioned that WP Engine does not allow for changes to file and directory permissions. Here are some other things that haven’t worked out so well for me, because I’m used to a traditional hosting environment (cPanel, unmanaged VPS, or unmanaged dedicated server):
No Real Cron
Yep, you can’t log into the control panel and set up real cron jobs. You may, if you’d like, use WordPress’ cron scheduler, but that’s not like real cron, because that cron scheduler is triggered by site visits. Real crons run in the background, and are triggered by the server.
Cookies and Sessions Crippled by Caching
At this point, it’s my opinion that WP Engine is for amateurs, which is fine but that’s not the case with me. Instead of great benefits, I feel their hosting environment is simply too restrictive. I’ve always felt that a web host should get out of the way and let their customers do whatever they want, unless there are security or performance issues that could potentially hurt their other customers. I can deal with the things I don’t like about WP Engine, but I’d never recommend or use WP Engine if there was another option.