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Wanderer is one of the best LS in the game, if not the best. It's very rare that I find a reason not to include it.

Even with so many common ways to negate it?

If it's negated, then it really doesn't matter which lost soul could have replaced it. 

What lost souls would be used in a type 1 57 card deck? I know you would need to know what kind of deck it is, but is */4 and FBTN preffered over the revealer and anti burial/ wanderer?

It varies considerably by strategy of deck, but there are definitely tiers of LSs that range from should be in every T1 deck, to heavily depends on strategy.
Here's how I would rank them, others can comment as they see fit:

Tier 1-Should be in every T1 deck:
Revealer: Not only is it possible soul gen, a first-turn Revealer can often tell you what strategy your opponent is using before the game has really begun.
Exchanger/Wanderer/Switcheroo: One of the best ways to access protected souls or swap for a nasty 2/3-Liner. It is also the best way for you to be able to rescue your own LS.
 
Tier 2-Should be in most decks, but may depend somewhat on strategy/other Lost Souls that should be included:
Fool: The fact is, there will be times when your defense will have to give up Lost Souls. So you might as well make rescuing those Lost Souls as painful for your opponent as possible. The only time I wouldn't include this is if you use fewer than 3 EEs in your deck. The beauty of this LS is that it doesn't matter if your enhancement is negated or not, it just has to be played. So you can use the most ineffective enhancement possible vs. a banding chain, and blow up the whole thing.
N.T. Only: This dropped out of Tier 1 in my estimation due to the new SoG, but it still should make the cut in most decks. The fact is, it still can't be rescued by well over half of the useful Heroes in the game, and its very existence forces a lot of offenses to use the Negater LS just for a chance at rescuing it.
Female Only: Basically the same as the NT only, except it isn't affected at all by the new SoG, and it is even more restrictive when it comes to who can rescue it.
Resurrection: I wasn't sure where to put this exactly, but I decided on Tier 2 because some decks just really don't care which Heroes they use, so recursion is not at all important. However, I'd say most decks do have 1-2 Heroes that are most important to their strategies, which means the ability to recur them when your defense gives up an LS can be important.
CBP: This would be a Tier 1 LS if EEs were more popular, but the fact is they are not. Still, the very presence of this LS can often scare off a FBTN Hero/Band, and it can be even better when it isn't noticed. I can't tell you how many times I've wiped out a band with Wrath/JiP/etc. because my opponent didn't realize they weren't preventing it.

Tier 3-Depends heavily on strategy, and what else you have room for:
Site Doubler/Site Guard/Site Discard/Deck Discard/Color Guard: All of these are relatively similar in usefulness, and depend greatly on your use of sites. They are also common in defensive-heavy decks, but unless you use at least 3 or more sites, none of them should be in your deck.
Negater (FBTN): This is a necessity if you use an offense that needs help accessing NT or Fem only, though it isn't as important as it once was with the new SoG. It can help or hurt you at varying times, so you need to plan accordingly.
Shame: I don't see this very commonly in T1 except in defensive heavy decks or multiplayer, but I think that's mostly because it is hard to fit in. It can be very useful, but it can also be worthless to you if drawn at the wrong time, which is why it is usually not picked over other LSs.
Thorns: Definitely more of a T2 staple for any defense that doesn't use DoU/SSS, but most often can't fit into T1 decks.
Speed Bump: Can be a sneaky way to block, but it usually does little good unless your opponent doesn't know it. If there was more ways for evil to force drawing, then it could be part of a great combo, but as is it's just a minor inconvenience that people have to deal with.
Shut Door/Beggar/Withdraw: All of these are pretty situational, but they can be nice in certain soul-hiding strategies. The Withdraw LS can combo well with Strife, but Strife won't be used much in T1 anyway.
Punisher: A lot of offenses use several colors, but it is pretty rare for a player to use more than three, and if they do, they have plenty of CBN Heroes (like Samuel or AutO) that aren't affected. There will almost always be better choices.
2/3-Liner: This went from being Tier 1 to Tier 3 with the rescue rule and dom cap combined, when it made it impossible to rescue your own shuffler with SoG and made Burial far less common in T1. It still has its uses when combined with Hormah/DoU, but it seems in a lot of cases, it just effectively becomes an extra LS available for your opponent to rescue.

Personally I think that virtually every deck should include:
2-liner/3-liner
Wanderer
1st Round Protect

Decks with more than 1 site should include:
Hand discard
Deck discard
Site doubler
Site guard

Decks with real defense should include:
CBP LS
New one that discards all heroes if you played a EE

Specialized decks should include specific LSs:
Demon decks = Demon discarder
Decks with all OT, male heroes (genesis, judges) = Negator LS
Decks with withdraw (herods, brown) = Withdrawl LS
Decks with LS hiding (pharisees, heretics) = focus on NT LSs
Decks that totally depend on 1 hero (Zeb, WS, Job, etc.) = new hero recur LS
Decks that totally depend on speed = anti-Burial (need all LSs to be available)
Decks with Abom = new LS that makes everyone draw 1 card

If you are not running any of the above and just need some generic good LSs:
Shut door LS (disappears when opponent plays a good dom)
Revealer LS (especially good in speed decks)
Female LS (the new SoG doesn't change anything here, so still good)

LSs that used to be good, but should no longer be used:
NT Only - there are just too many good NT heroes and the new SoG takes it
*/4 - the new SoG takes this too

On Revealer: I disagree that it doesn't belong in defensive heavy decks, as in the worst case scenario, it allows you to know what is coming. I don't think there are enough LSs more useful than revealer to usurp a spot. But I certainly see your argument.

On NT Only: It is true that there are a lot of good NT Heroes, but the fact is that this LS requires players to either use an NT offense (or at least an offense that includes NT Heroes) or use an effective method of stopping it. If you use this Soul, this souls and the female only both serve to limit your opponents options, which leaves you less to prepare for.

On 2/3 Liner: I agree that this LS can make or break a game, but it certainly shouldn't be Tier 1. Way too many times, it can end up biting you by providing another LS for your opponent to rescue, and if you don't use Burial, there's often not much that can be done about it. I suppose it could be Tier 2, but I think there are too many decks that are better without it to make it Tier 1.

On FRP: I can certainly see the argument, but I wouldn't make it Tier 1. It's protection is only useful if it is the only LS available to rescue, so if it isn't drawn at the right time, it's protection will expire before it does you any good. Maybe Tier 2, but I'd still put it at Tier 3 at best.

On NT Only: ...this LS requires players to either use an NT offense (or at least an offense that includes NT Heroes) or use an effective method of stopping it.

Red - both Centurions take it
Green - "called" Isaiah takes it
Silver - TSA, Gabriel, etc. takes it
White - all TGT girls take it
Blue - Genesis can NOT take it
Purple - all Disciples take it
Gold - all Luke/John heroes take it
Teal - PoC takes it
Mixed - probably have multiples of the above

So unless you're playing against a straight Genesis deck the NT's protection is unlikely to matter.  That is NOT good enough for me to put it anywhere near Tier 2.

Also, any deck that has the 2/3-liner should also have Burial.  The rest of our variances are probably just differences of opinion/style.

The issue is not whether or not a deck is capable of taking it the NT only, but rather that you often force players to use one of the above Heroes when their better options might be (and often will be):

Red-Ishmaiah, Ahimelek, Spy, or David
Green-Daniel+Mike, Samuel, Joseph
Silver-Captain of the Host, Michael (w/ Daniel), Seraph, Cherubim, AutO, AWSN
White-Obviously I am forced to concede this point 
Blue-Obviously you have already conceded this point 
Purple-I am mostly forced to concede this point, but I will address it later.
Gold-Samuel, Gideon, Jair, Ehud, Jephthah.
Teal-Every other deckable teal Hero.
Mixed-Almost certainly have multiples of the above

As for the issue with Disciples (and to a lesser extent TGT ladies) yes, you have a useless LS, but you are also able to design your deck to make up for that potential weakness. If you tailor your defense with the NT LS in mind (at least somewhat) then you have an advantage over primarily OT offenses, and you have an advantage over NT offenses. My thinking is that if you can limit your opponent's options, you have less that you need to account for on defense, which can be a game-changing difference. NT Soul allows you to do just that.

Also, any deck that has the 2/3-liner should also have Burial. 

Okay, but if you say 2/3 Liner is a Tier 1 LS, then you are also saying that Burial is a Tier 1 Dominant. I personally would have trouble fitting it into a 57 card deck, as in most cases there are 8 other dominants that are more useful (and/or less susceptible to Lampstand). I would only use Burial in a dedicated soul-control deck in T1 (such as the deck I recently posted).

I'm glad to hear people seriously misvalue lost souls. Should be an easy year at Nats.

Care to elaborate a bit more on this? It's not a very helpful statement unless people know what you are referring to...

I'll probably make a larger post with my soul preference later, but in the meantime, I don't think the NT is tier 1, and it's just barely tier 2. The fact of the matter is a large percentage of players (at least that I've played with) are using NT offenses, making the soul entirely useless except for NJ. A soul that won't even have a chance to matter in 40% (random guesstimate) of games isn't one that's necessary in every deck to me. Yes, in some games where people are using OT offenses, it can be helpful, and I would use it before the */4 soul  (but way after the Female Only soul), but even then, in more games than not, it's still not going to matter at all. The only exception would be in defense heavy decks that run slower.