I think Putin wants Hillary in. An extension of the Obama admin where he can further his agenda.
So if he says he likes Trump people may in his mind vote for Hillary. And if Trump wins he complimented him and maybe will start off on good terms.
The problem with your theory Hillary's first priority in Syria is getting rid of Putin's ally Assad, even if it means an ISIS and Al Nusra victory. She wants Syria to be a replay of Libya in 2011. Trump is fine with Assad in power and Putin bombing the rebels.