I'll be honest for Halo 4, the pre-order bonuses were good. However, the Limited version of the game was rubbish. Pretty much everything was later given to the players who didn't buy the limited. The limited copy never really had anything good in the first place, the only reason many people got it was because of the Season Map Pass, that discounted 3 DLC map packs, but this came disappointing as it later didn't include the Champion Bundle.
If I could have any sort of say regarding Halo 5: Guardian's pre-order bonuses/limited version, I would say keep to exclusive skins for the preorder bonuses or exclusive campaign skulls, and do not give them to the players who didn't pre-order. For a limited copy of the game, continue with the season map pass, have some sort of physical diary/map/something that gives a little bonus insight into the lore for the new universe, and other small little things.
The one thing 343i did right for the limited copy of Halo 4 was the packaging, that was very well made, and I just love the metal case that the game comes in.
But to be fair to 343i, Halo 4 was their experimental game, they didn't know how it would turn out, and used it as a learning experience. So we can know by the time Halo 5:G comes out, it'll be as great as they can manage.