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?
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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？"