Lets do some analysis... haha...
1. Headstock
Should have a neck support, so angled headstocks such as the Les Paul have adequate "space". Internal material surrounding the area in contact with the tuning heads, nut, and strings must be slightly stronger woven, to prevent scractching off the internal material (longer case life).
2. Neck
If there is a neck brace to have the guitar stay in place (not moving side to side or up and down or other awkward movements), having the guitar snug even when you're running after the god damned train / bus. Probably has something to do with the dimensions of the case, to hold it snug as well. With all the spare space around the neck, possible to have some little pockets to store maybe patch cables, secret stash of cigs, or whatever people can think of (no, I don't smoke).
3. Body
I think people would prefer a specified case to fit body dimensions of the guitar, snug. But this might take a toll on production costs etc. Dunno how you're gonna handle this... But having a one fit all is great. My Les Paul can sit in hardcase while I use the gigbag to carry my strat for gigs instead. Having sufficient padding on both the sides, front, and back of the guitar will be nice. I've noticed that memory foam type of thingy for my laptop case is really good, can absorb significant amounts of impact, while keeping my laptop snug. (laptop case is called zero something...)
4. Strap button
Most cases don't have this, and I feel this is a great addition seen in Chern's Spock. Having support for the strap button at the base is great in preventing knocking as we put down our guitars.
5. Additional features.
I know some people (like me), are rather minimalistic, so we don't have pedal cases, but would like to have the case to hold a pedal or two, cables, strings, tuning device/tuner. Having a laptop sleeve is also great, since some people do bring their macbooks to studio recordings or other stuff (hey, some of us are still within the educational bracket...)
Waterproofing is also a great addition. Considering its not exactly all sunshine here in Singapore. Also noted people like plush material for the rest of the interior of the case, but I'm not really picky, so as long as its cushy and comfy for my guitar thats fine.
6. User customisability
I'm surprised nobody mentioned this. But I'm a person who likes to have a wee bit of control of options on my bags. (I use a timbak2, heavily modified with strap padding, carabinas for my mp3) Having some add-on options will be nice. Such as having the straps in those clip on types, so I can sling / backpack my case, and of course hand carrying too.
Having additional things such as mp3 pouches as optional extras is a nice touch to user friendliness (some of us don't have SUPER long earphone/headphone cables to stretch from the laptop sleeve to our ears). Or things such as a little pouch to put whatever etc. (house keys) in.
Yeah, my 2 cents worth...