E.g. with the podcasts sync feature, you can only decide how many episodes you want stored for every podcast at a global level, not per podcast. So e.g. you can either store the most recent ten episodes of each podcast, or every episode of each podcast. So even though for most podcasts ten is probably enough, you end up needing to store every episode of every podcast on your phone even if there is only one podcast where you want every episode.
Similarly, once you purchase an app the only option is to download all the new updates, even if you don't use the app anymore. There is no option to archive the app, so it's either let iTunes keep installing the updates each week or else delete it the app you paid for from your computer. Again, this just needlessly churns through backup disks so that Apple can sell people more external hard drives.
These are just a couple examples, but it seems like pretty much every features of iTunes is designed to force you to buy more stuff from Apple that you don't actually need.