Guardian

1. Not really, though you could form a fleet of your guardians so you can use a hot key to select them, and then just hit the button.

2. Each ship can only have one guardian shield buff at a time. However, multiple guardians will cover eachother, allowing they to take some of the damage for the first gaurdian. However, you'd need to be in a massive battle to ever need more than three at once.

3. A fleet with about 1000 fleet points can fit inside a guardians area if you keep them really close together. Mainly used too make the "battle ball" where illuminators cluster around a gaurdian(s) with a mothership nearby.

4. Often a good choice, though repulsion field is one of the best ways to protect carriers and to stop the rare Heavy cruiser spam.

Subjugator

1. Infinite Void nailed it. I try to keep one for every cap ship I have. Not worth using on frigates, save maybe carriers.

2. Depends on what kind of enemies you are fighting.

Leaving Perseverance on autocast usually has these outcomes:
1. Subjugator perseveres a capital ship
2. Subjugator perseveres another Subjugator
3. Subjugator perseveres a frigate (usually Iconus Guardians, but I've also seen them persevere flaks)

The first outcome is the most preferable result, but they persevere other Subjugators just as frequently. They usually get to using it on frigates when they run out of capitals to use it on.

did they nerf the repulsion ability, btw?  it doesn't seem to be quite the bitch-slap it used to be...

It was not a little nerf, it was huge. 

But anyway, subjugator is hard to use effectively.  It needs micro mostly for the healing ability.  The other abiltiy can work if you put the ship on hold position, though it may still move a bit out of formation when it tries to cast it.  Idea behind it is to stop few ships that get through the repel.  It is most useful on a Heavy Cruiser.  The healing ability will remove disabling effects as well.

Repulsion isn't as good as it used to be but its still very effective for certain circumstances. in particular its great at keeping short ranged attackers like light frigates or heavy cruisers away from your battle-ball, which is filled with ships like Carriers and support cruisers that are, interesingly enough, very weak to light frigates and heavy cruisers.

its not as important an ability as it used to be but its still very good at punishing fleets of heavy cruisers. definitely worthwhile in my opinion.