I frequently need to find differences between two versions of the same db in order to create a script for migration. The way I usually proceed is to create a structure only dump in phpmyadmin and compare the results using WinMerge or a similar tool. This works great to detect new tables and columns but can be improved for changes in indices and foreign key constraints.
The main problem with the currently generated dump is that each ADD INDEX, ADD CONSTRAINT statement is generated in the order it was added to the database (I think). This makes two identical structures show up as different in a file compare tool because indices may have been created in different sequence in each database. If all indices and constraints were sorted by name, the lines would appear in the same order and not be marked as different.
I do not know if the order of indices/constraints can be important in certain situations - I can't think of such scenarios. But if that might be the case, the sorting of keys/constraints in a dump can at least be triggered using a configuration option.