Read some posts at nomadness.net or the Creative newsgroup. Scrolling thru long lists of songs, especially on a hdd-based mp3 player, is slow because the scroll wheel is small and has a slight clicking, and requires repetitive finger stroking. On the iPod, you can scroll thru 1000 songs in about 5 seconds, and still have the accuracy to easily pick the right one. Try that on the NJB3. Of course, this is only if the Zen is like the NJB3. At this point, there's lots of speculation anyway. And it's been said that the Zen is basically a shrunken version of the NJB3, so that's what I'm basing my thinking on.
USB1.1 is a negative because Creative should have just made it USB2.0, so that if you want FAST transfers you don't have to get a firewire card. Like Apple, they need to get of the firewire-high-horse and just make it easier for the consumer and make their products have USB2.0 (although in Apple's case it only applies to their computers).
Any decent filing system, such as the iPod's FAT32 or HFS+, has little defragmentation when used as an mp3 player. Remember that you don't use the mp3 player as a typical computer hard drive, copying files here and there constantly. It stores relatively large files that typically stay on there for a long time, so fragmentation problems should not even be a concern. Besides, battery life has little to do with fragmentation. It's has to do with having a big RAM buffer so the hard drive doesn't have to spin up or stay spinning so often. Whether or not the heads move back and for a few times isn't too important.
From what I remember, Creative decided to use (or continue using) a proprietary disk format because it would have support for large (>32GB hard drives that FAT32 doesn't support) and because the system makes cataloguing and organizing music easier. When you compare this to the iPod, there's really not too much of a difference in experience. But what goes on behind the scenes is quite different. The iPod just reads a simple database generated by whatever program that's used to transfer music over. This database file contains everything the iPod needs to display its contents. It never ever has to scan thru any songs and read tag info because all that work is done on the computer which has unlimited power and time. The NJB3's burden, I think, is in having to go thru and organize its contents itself. Plus, with a standard disk format, you don't need to run any extra software or drivers to tranfer data. It's really just plug-n-play. IMO, basically the iPod's software is much more simple and efficient.
Another disadvantage to the proprietary format is that the NJB3 requires drivers (not fun if they don't work in Windows), and it doesn't work on the Mac. The iPod requires no Windows drivers whatsoever.
The proprietary format was a curse since the NJB1. Things could have been simpler, easier, and worked better. Disk cleanups, getting stuck while loading, corrupted data, data loss, and driver problems could have been eliminated by using a standard disk format. I guess Creative didn't realize this with the NJB3, espeically when the iPod stood as a stunning example. I mean, how easy is it that you can plug the PC iPod into any computer (with firewire, which is a drawback, we all know), have Windows recognize it, then run the software on the iPod itself to transfer music, and be done. On the other hand, FAT32 is limited to 32GB, so Creative's format benefits those who want to have more than 32GB.
I don't think the last 3 negatives are the same. Poor customer support means if you experience technical difficulties, Creative isn't very helpful. Repair/replacement means if it breaks, you'll have to mail it in at your expense and wait a while to receive a repaired or replaced unit. For the iPod, you fill out an online form, Apple sends you a box overnight, you mail it off at no cost to you (overnight mail), they fix it or replace it the next day, and they mail it overnight to you, so you can have a new unit in as little as 48 hours. The warranty is self explanatory.
The iPod's SNR ratio is unpublished. But ask anyone here (a forum of critical audiophiles and audio enthusiasts), and they'll tell you it's very high, probably just as good as Creative's. Compare it between the Zen's 98dB, and I doubt anyone would notice a difference.
It's still only a dream to run apps on the iPod. The contacts/calendar info is marginally useful, considering that it's mainly an mp3 player that still doesn't have a queue feature like Creative (big drawback for some people, and for me my only major gripe).