The Envoys and Lost Souls

If it's the job of an Envoy to bring souls to the Mists, and if they have control over souls, then how can there be souls which remain in the mortal realm (like the Sunspears, or that one spirit hunting Xandra)?

Are they merely guides who check to see if a soul wants their help or not, and move on if they don't? Are there souls powerful enough to resist the Envoys command?

You know it's going to be pretty hard to answer your last two questions with an answer founded on hard quantifiable grounds. The envoys themselves make relatively sporadic appearances in factions and only in cutscenes. They didn't really say whether they go around asking souls whether they needed assistance or not going to the mist. As for the last question, Shiro is the only one known to have resisted them, though he was an envoy himself.

For your first question, my guess is that maybe it's because there is a gross disproportion of envoys to souls so it can take a while before a soul gets spirited away.

The Envoys are employed by the Oracle of the Mists (during Factions' time, Suun). This means that it is likely that they are not all that powerful (mass instant killing and resurrection aside) and most likely won't be seen outside Cantha (in terms of being in Tyria (the world)) - also note that within Cantha there are no restless spirits that we encounter - just those who are bound by ritualist actions (those in Tahnnakai Temple) who remain to guide those seeking aid.

Well, mass instant resurrection is within the realm of mortal magic (at least in GW1).

The mass death thing might just be a Shiro thing. I've always thought of it as a Meditation of the Reaper with no opportunity to break it, even if ANet hasn't shown us the actual meditation part. 'Course, it could have been a special envoy thing that the envoys can also protect against (hence why he couldn't do it to us again).

Meditation of the Reaper is actually a good explanation for what he does - if he goes through the entire thing, it's 600 damage, which is enough to kill most individuals. How he has the ability to do this is the question.

There's most likely a time limit during the final mission (hence "meditation") for two reasons:
1) He's mortal now, so it takes time to pull the stunt off.
2) Game balance over lore.

And true, I forgot about skills like Light of Dwayna that allows mass resurrection.

I'd always figured he'd just been invisibly performing it beforehand.

Until I thought of it as possibly being something that the envoys protect us against, but invisible meditation explains why becoming Weh no Su is so important even though we never actually fight Shiro in spirit form - he's always in contructs and things.

It's possible that for some reason fighting mortals while in spirit form is dangerous for him, so if they can see him to fight back he flees.