Saying that one employee is the least worst employee you have when someone calls you for a reference means they are the best employee. It also means you aren't particularly happy with any of them, but that's just adding a flavor to the sentiment that this employee is your best.
Now, if I asked you to recommend a bunch of project management/issue tracking software suites, and you absolutely floored me with praise for one, but said good but forgettable things about JIRA, that would be be damning with praise.
Coming full circle, saying that JIRA is the least-worst option means it's the best option and you just have an ideal in your head that isn't being met.
They're utterly different things, really.
But when I look at the landscape of tools that I've used that compete with or compete with a part of Jira, I just prefer Jira over the rest of them by an not-unsubstantial margin.
That said, Trello was great for a small team bootstrapping a new product without a lot of external dependencies or parallel release cycles and I hope they let them run independently.
> Damning with faint praise is an English idiom for words that effectively condemn by seeming to offer praise which is too moderate or marginal to be considered praise at all.
Which seems about right to me.
It's like writing an employee a letter of reference, and only saying that they're very punctual - meaning that there's nothing else good about them, other than the bare minimum of bothering to show up at work.
It seems to me that saying it's only good by comparison to how awful everything else is falls into this.