Wii disc images tended to come with multiple 'partitions' on them. For example, a single disc may have a partition for update information, a partition for the game, and in some cases (I think SSBB) partitions for game demos contained within the game. Nintendo had developers fill any space remaining on the disc after all of these partitions with algorithmicly generated 'garbage data,' just so each disc would be the same size once finalized and mastered.
As you have stated, a Wii .iso file (not actually an iso file) is just a 1:1 binary dump of the entire game disc, so it ends up being ~4.3GB in size for every game. A .wbfs file, on the other hand, is just the files contained within a single partition on the game disc - usually the aptly named "GAME" partition. The garbage data, extra game demos, and updates are generally left out, as in many cases they are unneeded.
As is always the case with backups and ROMs, the full, 1:1 and uncompressed dump will give you the least issues in all cases. The more compressed .wbfs format is fine outside of a few handfuls of corner cases, however.