In Avengers: Age Of Ultron, Tony Stark is the first member of the Avengers to get inside Baron von Strucker's castle, where he takes down a room full of soldiers before stepping out of his suit and travelling down a secret passage.
Why does he take off his suit in the middle of an enemy base when it might have protected him against Scarlet Witch's magic, or at the very least helped him better search the passageway with Jarvis' HUD?
1. The Avengers were unaware of the second enhanced at the moment: When Tony breached the shield and entered the castle, the Avengers knew only of "the blur". They later found out about Wanda. And since rest of the Avengers were already tackling "the blur", Tony let his guard down.
2. Greater maneuverability/Convenience: Tony wanted to check out the entire lab & all the computers, and the Iron Man armour isn't quite the tool to do it with. He had already run a thermal scan of the entire area, and since it was clear, he had no reason to believe he would be in any kind of danger. He wanted to check out the computers by himself. (And after watching Iron man 3, I believe we all know how ridiculous it is when Tony tries to walk around in that armour :P)
3. The Armour was in sentry mode: Tony had put the armour to sentry mode, which essentially meant that he had J.A.R.V.I.S. looking out for any danger. He could summon the armour any time he needed it, as he does whilst reaching out for the scepter.
To summarise: Tony believed himself to be in a condition safe enough to come out of the armour, considering the information that was available to them at the time.
Stark07's answer here is perfectly correct when at looks at the reasons from Tony's perspective about why he leaves the armour behind, but I think this is worth digging a little deeper into. Tony Stark is one of the most well developed characters not just in the Marvel Cinematic Universe, but in modern cinema today, and his relationship with his Iron Man suits is as fascinating as it is unhealthy.
If you recall the events of Iron Man, you will remember that Tony Stark first designs his Iron Man suit (and later refines it) in order to escape captivity in Afghanistan, where he was being held by the Ten Rings terrorists. It doesn't take many rewatches of Iron Man and Iron Man 2 to see that not long after his imprisonment, he begins to suffer from PTSD (post-traumatic stress disorder) - simply look at his actions in the films, almost all of which are motivated by a greater need to "take control".
By the time Iron Man 3 rolls around, Tony Stark is in a worse state than ever after flying through the portal in The Avengers/Avengers Assemble. It is here we see his PTSD at it's worst state - he is quite literally a mess, having panic attacks if asked to recall the events of New York and spending increasingly large amounts of time building more Iron Man suits, to the point where it is putting strain on his relationship with Pepper Potts.
The events of Iron Man 3, which leave Tony suitless and force him to rely on himself rather than the suits for the first time since Afghanistan go a long way to easing some of the worries he faces - most importantly, that HE is Iron Man, not the suit. The end result of this is that by the time Avengers: Age of Ultron rolls around, we find ourselves in the company of the most mentally sound version of Tony Stark we have seen since his first appearance in Iron Man - at least until Scarlet Witch interacts with him.
Tony Stark's PTSD and his new found ability to cope with it is the reason that he takes off the suit in Baron von Strucker's base. It's a way of showing the audience that Tony Stark isn't as reliant on the suits as he once was - that he is "better", so to speak. He feels confident that he is relatively safe without the suit, and as such he leaves it behind - but not too far behind. He is Iron Man after all.
Below are the answers from an out-of-universe perspective.
1) To keep the story moving forward. With the suit on, Tony Stark cannot be brainwashed or the brainwashing is less convincing to the audience. Brainwashing a suit of armor would look stupid, something Michael Bay would do.
2) Stark is the oldie and Witch is the newbie. The relationship must start very early in the movie, and it must begin human to human.
