Personally, I don't think we should be allowed to change our team once the tournament has started (especially since it'll take place over a couple of days).
I think that, when the tournament starts, we should have to send a PM which has our pokemon and their movesets, as well as which version of the game we're using (X/Y or ORAS).
I've never been in a pokemon tournament before, but I have been in TCG tournaments. Though the use of side decks can be used between matches, what we have in that side deck and our main deck can't be changed between matches (be it a Swiss-style point system tournament or a knockout tournament).
To me, being able to change a pokemon team mid-way through a tournament would be like switching to another deck mid-way through a TCG tournament. Changing a moveset between matches would be like swapping out cards from the side deck, but changing any members of the team has a sort of cheat-ish feel to it.