1. People often prefer the OEM software skins i.e. sense and touchwiz over stock android, IMO all of the apps are far better than stock android ones, stock android is too limited/minimal and the touchwiz and sense version of the camera, gallery, calendar are superior to the stock android alternatives IMO, each software skin has its own nice wee features like touchwiz smart stuff (although you get most of these things on the market now)
I prefer sense to everything else.
Only thing I like about stock android is the holo theme throughout.
2. Camera is better on the X, S and GS 3 overall
3. design is personal preference, IMO HTC phones are the nicest for design, especially the build and premium quality. I dislike the design of the GS 3 and it is the main reason why I haven't moved to one.
4. storage is a factor too, many people rule out the nexus devices and the HTC one X and S purely due to there being no SD slot or/and limited internal storage
5. Some people want a removable battery as they might travel a lot so having a few spares on you would be much better than having to charge at every chance available
6. screen quality and size, some don't want phones any bigger than 4.3" and some may want a much bigger screen like the note II
then you have;
LCD:
pure whites, natural colours, sharper/clearer, more power efficient on bright colours
VS
SAMOLED:
true blacks, saturated colours and better viewing angles overall, more power efficient on dark colours
Contract prices for the nexus 4 are actually similar to the other top end phones.
If I didn't have a budget, I rather have the one S, X+, XL, note II (if size wasn't an issue) or GS 3 LTE (if the design wasn't an issue)