According to this site, both 能 and 可以 can be used to politely ask for permission.
1) Which is considered more polite?
2) Which is more formal?
3) Is it the same for Cantonese?
For the 'asking for permission' function, 能 is similar to 'can' and 可以/可否 is similar to 'may' in English.
Strictly speaking, 'may' is the proper word to use and is considered more polite and formal, for example "May I ask you a question" but in casual day to day speech, more and more people think replacing 'may' with 'can' and say "can I ask you a question?" is acceptable. I would still suggest you use 'may' (可以/可否) instead of 'can' (能)
Cantonese do not use 能 or 能够 when ask for permission. We say "可以" as in "我可以問你一個問題嗎？" which is a polite way to ask. To be more polite, we would say "我可唔可以問你一個問題？"
In Mandarin, "我可不可以問你一個問題?" (more colloquial) or "我可否問你一個問題?" (more literary) are the more polite form compare to "我能問你一個問題嗎？"