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What's the difference between the に祈る and を祈る forms?
Like what's the difference between (1.) and (2.):
EDIT: What's the difference between the ように祈る and のを祈る forms?
Like if what I want to say is "I pray that he will recover quickly", what's the difference between (1.) and (2.):
早く治るように祈ります。
早く治るのを祈ります。
1) うまく行くのに祈ってくださいね。
This looks strange. I'm not sure where you found it. のに means "although" making the sentence sound like: "Although it goes well, please pray."
I think you're confused with ように indicating a goal.
Most prayers are formed like this: うまく行くように（祈る）。
2) うまく行くのを祈ってくださいね
This is the correct form for the transitive verb 祈る
Can also replace の with こと
EDIT:
1- ように indicates the goal. You pray so that things goes well. Prayers in temples are formed like this and many people before an exam for example or before a speech will address a prayer like this. (no need to be in a temple) The verb 祈る is sometimes omitted.
2- Vb + の/ことを祈る
This is more of an everyday hope expression, a wish for luck. (second meaning of 祈る is "to wish")
Most people will translate うまく行くことを祈りましょう as "Let's cross our fingers"
You can also say: 成功を祈ってね -> "'pray' for my success" or "wish me success" Or something like:
頑張って！成功を祈るよ！
3- And thanks to istrasci for pointing out that using only に indicates to whom you address the prayer: 神様に祈る
1) Pray so that it goes well
2) Pray that it goes well.
This quite direct grammatically speaking. Nothing fancy here. に is the aim of the prayer, and を is the content of the prayer.
