Caveat: Firstly, let me just say that I do like most of the way the main rules are now in1.2 - it's not perfect but there are not many things dreadfully wrong. The team are putting a lot of work in, but the direction it has taken is not how many would like it to go.
What is putting me (and a lot of others off) is that the Army Books took massive hits across the board and a great many of the changes make no sense fluff-wise, changes appear to have been made solely in response to ETC tournament data that do not translate well to casual players.
There's an awful lot of math-hammer and not much accounting for hobbyist's creativity.
Prime example: the ethereal rule. This was reportedly changed in response to ethereal spam appearing in a tournament. Ethereal units got a heavy nerf, no price reduction a new rule that makes little sense fluff-wise. Why can you now easily kill ghosts with arrows?
It makes wraiths poor and phantom hosts unplayable.
Banshees are ridiculously expensive now.
This ethereal spam would never be seen in 'casual' play but the change was made to the detriment of casual players.
Other things like the removal of unit weapon/upgrade options, or the auto-include of other options were made to streamline play so tournament players knew what unit did/had what. While that might shave seconds off a tournament game, it removes the ability to tailor your units and army to your own vision or story of your army, e.g. varkolaks can no longer have fly, Monstrous revenant now auto-includes fly (with associated points cost).
Vampires are pathetically weak in combat and not particularly great spellcasters which just doesn't match most people's concept of what a vampire should be.
The drastic reduction of magic effectiveness is a heavy hit to a magic-heavy army like ours and the hobbling of the ability of VC to raise troops has impacted gameplay and isn't fluff-compatible.
This sounds like a big moan, but you asked for examples and these are just a few off the top of my head.
Removal of customisation options might makes things faster, but it makes things cookie-cutter and restrictive. (That's what Kings of War is for)
This hobby is imaginative after all, and it just doesn't sit right.
A big problem is that the character of the armies was not considered when they hit everything with the nerf bat and it upset a lot of people. It's difficult to get people enthused about it now.
If/when character-considerate army books are released it might be a different story but as the game stands in its current incarnation, it just lacks the fun of a personal story-telling element.