In the first movie the crew consisted of:
Morpheus
Trinity
Joey Pants
Dozer
Tank
White girl
New Zealand looking guy
Mouse dude
Neo

Then Joey pants killed off White girl, New Zealand looking guy, Dozer. So that is 4 down. Mouse dude was offed in the Matrix. Tank was killed sometime between movies.

In Reloaded we have the addition of Link. So the replaced 6 people with one.

Seems like the ship that contains the One would be the most well crewed. Especially since they've freed so many people from the Matrix in the last 6 months. They must have been extra busy.

I presume you mean

Morpheus
Trinity
Cypher
Dozer
Tank
Switch
Apoc
Mouser
Neo

Morpheus answered your question when he spoke to Link. He now trusts no one after Cypher turned traitor. He hasn't bothered to acquire more crew. Besides, he has Neo.

Ah, missed that bit of dialogue.

Well, it was indirect. There was some other stuff that hints at that, as well.

Like the captains don't answer to anyone, not Lock, not the counsel...unless they want to. So it is totally Morpheus' decision to add crew.

And somebody else talks to/about him, maybe Niobe or maybe it was Link talking to his puss....uh, wife, about Morpheus' trust issues.

It all adds up.

Good question, bad answer. While I don't think we saw MUCH of thier activity, I would think that the crew members had important duties.. obviously since Neo is there the need for too many people just to go into the matrix isn't probably a necissary (eliminating need to replace Cypher, Swith, and Apoc), but I'm pretty sure Dozer and Mouse ran systems on the Neb. I would think whay they did would probably need replacement..?

Doesn't the "kid" mentiont that Morpheus is still in the process of adding his crew and that he wants to apply when he is old enough?

he just says that the positions haven't been filled yet

I assume they only need one operator. The rest are extra. Since in the Logos (Niobe's ship), they only have Niobe, Ghost, and Sparks (operator).

To expand on this a little... We see a few ship crews in reloaded and they all have 3 or 4 people. This number looks pretty standard right? So why did the Neb have so many in the first movie?

Because they were searching for the One, and that required more Matrix missions, and more people to go on those missions?

I thought it was Epoch, not Apoc...

It's Apoc. Check IMDB:

http://us.imdb.com/Title?0133093

And look at the cast list.

Mouse ... not Mouser.

Oops. Could've sworn they said Mouser, and I never checked the credits. Oh, well.

I'm not so sure the other ships had so few, we never really saw everything at once. The ship destroyed (that we see) at the end of Reloaded had 5, 3 were in the Matrix, 2 on board when the sentinels blew it up. Can't remember names at the moment.

Wow, I don't mean to sound like a prick, but that's some major misspelling right there.

It's phonetic enough to get the point across.

Mouse ... not Mouser.

Mouser got offed in SMB 2.