Differences migrating using Target Mode vs Migration Assistant on source machine?
If by Target Mode you mean loading the HD of the old computer onto the new computer and drag-dropping files, then the difference is that Migration Assistant knows what it is doing.

You could have done this in the old Mac OS Classic days, but now there are tons of hidden files and locations that you would never remember to transfer over.

You should really use the migration assistant unless you have a good reason not to.