It's a great debate, I think this is the first year we can actually take this comparison somewhat seriously which I guess is why the media is taking renewed interest in it, especially with Thurston well on track to his 4th Dally M. Unfortunately it doesn't take long for the bitchiness and pedantry such as claiming 1.5 premierships to come to the fore in these threads.
For me their attack is close to on par, both possess immaculate kicking and passing games, although Johns' array of kicks he was able to perform with accuracy may put him slightly ahead there. Thurston is a better goalkicker though.
As others have said, defence-wise Johns has Thurston covered pretty comfortably, although Thurston has improved in this area and has a nice round-the-legs tackle when he's prepared to use his shoulder. He can still be a liability in defence though which Johns rarely was.
Career-wise, you have to take premierships into account, even though it's so hard to get one. If Thurston seriously wants to go down as an all-time better halfback than an immortal in Johns you'd think he has to nab at least 1 premiership.
It's tight, but if I'm picking a team to play for my life Johns just gets the nod over Thurston. He's just ever so slightly the better all round player. He didn't really have an exploitable weakness.