The Fill Queue is in the queue menu if you can't find it, the same one where you can sort the queue.
As a rule, every new feature is off by default. You have some good points that stuff shouldn't be thrown in just for the sake of being thrown in. But in this case, an option to automatically add pets as you learn them would get tucked away into the options list out of the way, it wouldn't require much work, it wouldn't impact the size/performance of the rest of the addon, and it would require little/no maintenance once added. It's a decent candidate for a new feature, especially if it can be made useful for a wide audience.
Feature creep is something to definitely keep in check too. Everything added has to be supported for the life of the addon, so extra thought goes into what (and especially how) they get added. And if it's any comfort about addon bloat, grab an addon that shows addon resource usage. You may be surprised at how little memory Rematch uses compared to others.
Maybe change the first one to Only pets I don't already have @ lvl 25 or in the queue.
That sounds good. I'll probably have a toast appear when a pet is added to the queue (much like when leveling pet changes after a battle) if the 'Hide toasts' option isn't checked too, so there's less mystery about whether a pet got added or not.
Do you think this should also kick in when you stone a pet? Personally, if I'm upgrading a pet to rare I probably want to level it, especially if I don't already have a lvl 25 version.
I think so yeah. Perhaps with the 'Only rares' option.