but he's quite often leading rosberg after the first lap so qualy isn't such a big issue.
I don't know, is Rosberg the objective here? If Mercedes were 1-2, and Schumacher was second, then maybe; but as things stand, qualifying well is the only way of getting close to a podium, given the car's current ability.
This is what has helped Rosberg so much - along with the better and mainly safer strategies. If you look at the number of positions gained by each driver, then you'll see Rosberg generally gained 1 position during the race (4 times) - only in Great Britain and Europe did he gain two positions and in Canada four. As such, adding up the gains/losses from his grid position, you'd get a rating of five.
Schumacher also has a rating of five, despite having the by far better starts. But given that his starting position is so far back, Mercedes seem to pick up the weirder, riskier strategies, and up to now it hasn't paid off at all.
As Urawa pointed out, the problems arising with the emptier tank are the main issue, and while they can be somewhat controlled during the race, their effect on qualies is far too great. The last four races have been such chores, starting from worse and worse positions, it's truly frustrating and I really don't know what it will take for things to change.