Based on the cleaner roms out so far, there is only a 500mb savings from the stock firmware. Cutting below that tends to impact stability of the device, so will be a while for roms to evolve past this. Getting the Google version for firmware might yield more- when stable for other S4 models.
Seems real simple to me. If you have only about six GB of apps on your current device, the 9gb 16 model will probably be fine (with apps2sd update). If you have a 32GB now, and are anywhere near 9GB, you probably will not be.
Seems better to get the $100 more device (or $50 more if paying full). Look at the total cost of time and effort. With the 32GB version, you are DONE. No rooting or other issues like waiting for a dev that may NEVER support data to sd. Seems the $50 or even $100 is a bargain from this perspective. No jumping through hoops (and perhaps bricking/tripping) since already 15GB more storage that is also faster.
From a true total cost standpoint, IF you have many apps, the 32GB verison seems an absolute no brainer. Even if you root, it seems to make more sense. Less issues to deal with.
Added: That reminds me of an assertion someone made that their sd card is faster than internal for app performace. An obvious placebo, since the device caches for operation of apps in the internal storage, regardless of where the app is. This would mean that even IF the sd card were faster than internal, the bottleneck is still the slowest part of the direct chain/path to the chipset (the internal storage is more direct to the chipset).