I don't see the problem.
"Thy will be done", yes. I can always have that stance towards God, meaning that I trust that it will all work out in the end even if times are hard right now, even if I feel desperate and hopeless. It means that I always can trust that there is a long term plan and purpose. But what if God also wants us to act as independent beings and act upon our feelings and thoughts, and what if he allows us to sometimes ask him for a different outcome? God had a plan that would work out well but now I as his child asked him to modify that plan a little. It's not a big deal.
God created the earth which is in a very unperfect state right now (this is undisputable from a biblical sense and I think it's important as a background for the "Thy will be done" stance). Every human being has a life. Everyone with different pre-conditions, some seem fair and some seem very unfair. Who knows what the purpose is, but perhaps this short life on earth is some sort of test before we die and are judged, a test that will have consequences for the afterlife.
What if in this simulation, a human's life on earth, an individual stumbles on a problem he feels he can't handle. He loses hope. Why doesn't it make sense then to cry out to God and ask him to change the outcome? Maybe the answered prayer and changed outcome will have effects for this individual's state in eternity (a smaller reward in heaven perhaps), maybe not, but I think it makes sense, praying makes sense