Should people have to apply for magical abilities? Yes, but it should be a streamlined process. If we stick to canon abilities, have a limit on "rare" abilities and have it make sense IC. I think with more advanced/rare abilities that could significantly impact character power or relationships with other characters (so like legilimency, wandless magic etc.) there should be clear guidelines and limits on how many characters one player can have with those abilities. It can be flexible and on a case-by-case basis too, but there should be clear communication and IC continuity.
Should we keep character roles simple or expand them further? Expand as needed, I suppose? The only concern is, again, roles being hogged, so maybe limits to how many significant roles someone can have (e.g. only one Hogwarts professor per player, two student roles per character etc.)
How do you think we should handle magical items? Unpopular opinion but I'm not a fan of non-canon magical items at all. I think sticking to the lore and keeping it simple works best and prevents complications.
Ways to prevent people from overpowering their characters. Just being sensible about it, I guess? Limits on magical abilities/ important roles per character. Ensuring no one character or player has a monopoly over one whole plot/institution. Clear communication about aims and weaknesses in the case of big players, to ensure no-one remains completely infallible or at least that there's some IC logic/purpose to it. I think the main concern is when overpowered characters severely limit other character's choices/plots in some way that isn't realistic and serves no end goal apart from keeping the character powerful and untouchable indefinitely.