The truth is there is nothing wrong with QTEs and experience systems.
But it's a misconception to stop there. The truth is - game design is an art. There is no recipe of A + B that gaurantees C. If you take QTEs, you can make a great game. If you take expeirience systems, you can make a great game. But if you take QTEs and experinece systems and put them together in the same game? You can create an unfun mess.
Anything can be fun. Regenerating health is not a sufficient reason to hate modern FPSes. But it's regenerating health in conjunciton with other mechanics and design - like an emphasis on cover-based popamole, or an overly simplistic level design (corridors, instant-death zones for not following orders, etc) that when used in conjunction with regenerating health... Right, you get the idea.
The problem with the new Thief is it has no apparent design consensus. Garrett is a master thief, so why does he need upgrades? What do we find fun about upgrades? Who knows. They're just doing it because CoD and WoW have experience systems and are successful / popular. They're not doing it for any better reason than that. It's this shallow reasoning, and the lack of a true motive, that hurts the game.
Thief should be about being sneaky. It doesn't mean duck-waddle (Thief 1 can be played by running, jumping, sprinting, hopping, climbing... very little 'forced' creeping and crawling), it just means you aren't running forward down a burning hallway in bullet time with red jelly plastered all over you until you reach an exit and need to press a random button or you have to start over from a check point for failing to activate the QTE. Thief should be about exploration, discovering secrets, and acquiring wealth-items. Thief should be about avoiding combat rather than confronting it head on (though this doesn't mean there can't be sections where direct confrontation is a bad thing). Thief should be about using various tools (in the forms of arrow types and potions) to overcome certain obstacles. Thief should be about variable mission objectives (with three levels of difficulty, to satisfy all sorts of playertypes).
The Thief I've seen so far is none of these things.
Developers should pursue what they think is best. We aren't the developer, so it's technically 'none of our business'. Publishers have a right to demand things, because they control the purse strings.
But it is absolutely not sensible to do what most modern game companies do. Ignoring fan feedback and desires is sure to hurt a series' longterm profitability. Creating content that is barely indistinguishable from market leaders is a horrible horrible idea - Ubisoft is already shitting out three assassin's creeds every 4 quarters, EA is already shitting out a new Battlefield every 12 months, why are you copying these people, who are already oversaturing the market with their own product? Your inferior copyclone isn't going to do better, nor nearly as good, as its direct competitors.
Making a shit game hurts your reputation. It certainly doesn't gaurantee a profit (look at the mediocre titles Square's already shat out - Tomb Raider and Hitman did not make more money despite playing along with modern design conventions - they didn't even make a profit). It certainly means there won't be a sequel, not that developers are forward-thinking enough to care about the next game they have to make after the one they're on ships.
Publishers control the money during production, but that's our job once the game's out of production. Our opinions do matter.