I'll never change anyone's mind on click mez, but I swear to you all that it's not some huge problem. You don't need to set it on auto.
The duration vs recharge on the clicky mez powers is very generous. It's not like Hasten where you're going to just barely get it to perma, it'll be recharged before the duration is even half expired. So you don't need to watch like a hawk for when it comes off recharge. You've got time.
What I do is try to check it right before I dive into a new spawn. If it's off recharge, I click it, then ignore it for the duration of fighting that spawn.
If you do end up with a gap in your mez protection and you get mezzed, it's NBD! These powers can be clicked through mezzes which breaks you free.
For Shield, you plausibly want to set the power on auto because it drives your DDR. For SR and Ninjutsu it's fine to just click it between spawns.