We originally decided to use Trello because GitHub Issues were getting way too crowded and overwhelming. Also, GitHub Issues are great for detailed bits of work, but they're not so great at high-level tasks or buckets of work. The milestones stuff in there just doesn’t cut it.
We love Trello. It's great because it’s super flexible. Almost to a fault. The one thing I wish it had: velocity. Not sure why they don’t add that, but I would so use it. Right now we just add an estimate of hours at the top of the description field. I also wish they had a more robust Calendar and concept of time. Trying to get Trello to act like a product planning tool is almost impossible. And using other tools is a nightmare. So we’re kind of stuck using Trello as-is. But Trello as-is is > all the other PM tools we’ve tried (and we’ve tried a lot).