Yeah specifically I am worried that I singling out a character. See I have an Astropath Transcendent, he has sensory deprivation. I usually send a single big ad at them as some of them have been very powerful(( we are literally in the middle of the entire crew Explorator, power armor wearing arch militant, Navigator and astropath are fighting an Eversor assassin, I have a Ascension level scum who is an amassing gunslinger with them. ANYWAY the thing is I did not realize that the Eversor had “from the beyond” and thus made it immune to the ability sensory deprivation. See several times I have sent creatures that are immune to psychic abilities or telepathy (( last time were flesh hounds and blood letters)) well I decided that since the Eversor was once human and had a human construction of his mind he would not get the full blind deaf dumb thing but basically -30 to BS and WS. But he said he was tired of things that were immune to his mental abilities. I think I do have a prejudiced against them as he can walk into any social situation and dig into people’s minds as he has a massive will power score.

I guess I just need to work a little more on being fairer on it though maybe I should use large groups of bad guys instead of one with a lot of immunities.

I don't think you are being unfair to the astropath. Psychic powers are well known in the setting, and if the PCs astropath is using SD when ever he can people will take note of it. So it stands to reason:

A) If psychic powers are known NPC will cultivate means to counter such powers. If SD is as powerful as it's written and it's a common power, then NPC will com up with counters just for it.

B) If the NPC know they are going up against the PCs they might do a little research. If the astropath is always using SD then they will be able to find out about it. (For example by bribing members of the PCs crew.) In any case it stands to reason if the PCs knew they were facing an Astropath they'd be ready for SD.

From a meta-game perspective it's a downer for the astropath to always just strike the big bad blind and deaf. It makes for boring final encounters. On the other hand for an Astropath it's hard not to be able to use him powers. As you are playing the class to use cool powers, and you generally don't have a lot of combat powers that are better than say a storm bolter, melta or plasma gun. When I'm GMing I may sure that major bad guys have good will power, and the resistance talent. Unatural will power also helps. As do hexgramic wards from IH. Finally the main bad guy has fate points too. That way the psyker has a chance, but it's still a struggle, and the players will be thrilled it works. If all else fails have a good backup plan for big bad if he loses. Sure he might not know that he'll be facing the PCs, but a worthy bad guy has a plan for the case he is blinded.

PS- If the player becomes a pain about you reigning in his power to acceptable levels. Just start having the big bad have a psyker side kick. After all if any power were that useful wouldn't every psyker work on developing the power, and wouldn't everyone be taking advantage of it. After a few encounters I find the player are begging to limit the power or find a good counter. (Which you can start using as wouldn't some one have figured the counter as well...)

I'm going to start with a short story. My first D&D game, my first character. I was 16:

I rolled up a valorous Paladin, righter of wrongs, noble, white cloak, the whole bit, and I was excited and rearing to go. The DM proceeded to run a game where he could never do the right thing and was humiliated every time he tried. His powers and abilities were useless, his moral code repeatedly pointed out to be silly, and apparently the magic users in the world hadn't heard of heavy armor because there was always a magical elevator around to him on his face or magnetic room to pin him to the ceiling.

One of the most important rules of GMing is to make the kinds of stories your players want to be in, and you can tell which kind of stories they want by looking at the kind of characters they made. You bend the story to them. Swash buckling captain? Swords fights and high adventure. Super intelligent senchal with lots of trade skills? Economic intrigue and empire building. Void master focused on piloting small craft and a big pistol? Han solo.

Astropath who uses lots of social powers and non direct damage attacks? I'm guessing wants to be a manipulative wizard, and no, you probably shouldn't be summarily removing that players ability to do anything, and the only thing they are useful at.

I admit, astropaths can be hard, I'm struggling with how to handle ours. At the same time, BBEGs shouldn't be that easy to nullify, and psychic defenses are readily available. So how do you give him the kind of story he wants without letting him dominate?

I would say you need to perhaps be more creative. I think the answer is increased creativity and complexity.

Instead of making him ineffective, change the situation. Does there have to be a BBEG out there facing them, and does he need to be the toughest one on the field? Some of the best villains aren't the toughest opponents. Can you make situations more complex so that the main goal isn't to "kill the bad guy". Can you give him things that are more important to do? What about having lots of opponents, making them be racing against the clock?

Can you make social situations more complex? Maybe just getting someone to like you or getting information out of them is only part of the challenge. He helped, which is nice, but it doesn't end the situation. The information can be wrong, or planted. A savvy villain will know what astropaths are capable of and plan for it.

Finally, come up with short encounters that he can excel at and it doesn't hurt anything. Put in information gathering or social situations you EXPECT him to bypass easily. He is the square peg to go in the square hole of the story. Cut out character shaped holes in your plot, as they say.

In short, come up with situations where he is still useful and is free to scheme and manipulate, but don't break the game.

Again, you are the DM and it is your job to make the kind of story your players can enjoy. You should never rob a player of the ability to be effective.

An older experienced GM told me once, "It isn't the GM vs the Players. It is the Players vs the World and you are the judge."

I read a book by Tracy Hickman (of D&D fame) called X-DM. I thought it was a useful book because it discussed the various players he had come across over the years and the expectations those kinds of players have and how to fufill them.

As a GM, I find that telling the story is important, but I have to remind myself that it isn't MY story. It is the player's story and that I am there to give them focus and to let them play what they want to be. Obviously, you make it a struggle. Free things are worthless and will be treated as such. But if they know you aren't delibrately screwing them over, then they won't revolt when a bone-headed plan results in pain and suffering. They will know that they didn't plan correctly instead of feeling like you are shoehorning them into your story. Sometimes you make a mistake as a GM (*gasp* I am admitting it!) but you can overcome by adapting the mistake to the story. Are they "overpowered" because of something you allowed them to find easily? Add a hidden cost to it (daemonic, the prized posession of a rival rogue trader, Archaeotech that the Mechanicus will kill for...etc. Makes the story more interesting when they have to decide if the awesome thing they have is worth the negative attention.

For the most part, player happiness is a subtle game within a game for me. Looking at the character sheet to see what they want to do (skills..etc.) as riplikash said; watch how they behave when you present them with certain scenarios, are they excited or bored; what do they keep trying to do? Are you letting them? Why not? What can you do to get that edge of the seat feeling from them? There is another great post about GM tricks and tips. I am definitely going to steal all of them. (Programmers rule: Why create new what you can borrow (legally) from someone else?)I will admit that sometimes it isn't subtle. Since I run my game only once a month, I ask after every few games if folks are having fun and then I adapt the story we are playing to make it closer to the story they want to play. I have had GMs do neither. I have had GMs ask after each game. Up to you.

If your astropath feels neglected or useless, you need to work with the player to make them feel special again.