Honesty=/=Goodness. Nor does he take sides.
"Can you free me?"
"I can...but will I?"
Varys wants the good of the realm by which he understands peace. People don't give a shit who's the king as long as there is peace and they can live their lives. He isn't a hero though. He will do all he can to ensure the good of the real but he will stop at the very moment something that he has done might implicate him or cast a light on him.
I wasn't saying honesty and goodness are the same thing. I'm saying that if he is being honest about wanting the good of the realm, why has he not taken opportunities to remove people who are harmful to the realm and put people in power who aren't? He just sits back and let the Lannisters be dicks to everyone.
Say Varys has every Lannister assassinated. Now what? What does the kingdom do? Stannis steps in. What if he's a dickwad too? Should he have him assassinated too? And then what? Keep the throne for himself? Determining who's going to be the king is not the job he has chosen for himself. Neither is dispensing justice. He provides information and a voice of reason for whoever sits on the throne. Good or bad.
Stannis was known as a just man before Melisandre came along, even if people didn't particularly like him. And I thought it was assumed Varys would get rid of him too because he doesn't like magic. Making Renly or some less megalomaniac "for the family!" Lannister king. And determining who's going to be the king IS the job he's chosen for himself
if he claims to want what's best for the realm.
I don't believe in his honesty about wanting what's best for the realm because he is passive and doesn't take the opportunities he has to put the good people in power. He prefers to make simpering faces while claiming his hands were tied. How exactly would he have been implicated if he let Ned escape? I was under the impression that he was visiting him in secret. Plus I will not let it go that he was planning something early in the first season and we have yet to see the fruits of that plan or hear mention of it again.
At the very least, his idea of what's best for the realm is questionable because he seemed to be advocating war with the Dothraki and we don't know if he means long term peace or short term peace.
"We will be at war soon, my friend."
"What good is war NOW? We're not ready."
http://www.youtube.com/tv?v=aDnbHTcBWbQ
Not really a conversation someone has if they care about the immediate good of the realm. He has plans. He is not honest. Or his honesty is a murky, grey honesty.
ETA: Isn't it wonderfully convenient that he told Jorah he'd received his pardon just in time for Jorah to decide to stop the assassination attempt? If he wanted to assassinate her, why not notify him after the fact? He claims to want something but takes actions so that it doesn't happen. Just like he clearly knows its true about Joffrey(
http://www.youtube.com/tv?v=x_WQUOHZ6Dg), but doesn't free a man who could be in a good position to act on that truth without implicating himself. Just like he doesn't slip a note to Robb warning him about the wedding. In that clip with fat guy who's name I can never remember, he says "Delay, you say; move fast, I reply." What makes Drogo determined to attack Westeros sooner rather than later? The assassination failing.
Now I know I'm making a huge assumption by side-eyeing the timing of Jorah receiving the pardon, but it seems to me that Varys is pushing for conflict, not peace. He seems to be inconsistent, from my point of view. Instead of telling Tyrion flat out that he needs to be working to make the realm a better place, he tries to slip Shae some diamonds under the table. All that did is make her even more angry with Tyrion because now she thinks he's being a coward and letting Varys do his dirty work (that's how I understood the scene anyway). Whereas he could have had a straightforward conversation with Tyrion about the dangers of keeping Shae around any longer.