It's funny, I didn't see any mention of Red Dead Redemption? I loved the GTA games of old because they're sandbox was new and unexpected. There were hidden mini-challenges back then, often without much explanation. Mayhem missions, hidden races. It was worth exploring. Nowadays a lot of those are trophy/achievement checklists. Plus the world is so "real", commuting in them isn't much fun. The random joy of annoying the cops and spawning spontaneous car chases got old quickly. The incongruity between story missions and open world missions was jarring.
But Red Dead took some ground back for me. First, the world wasn't your generic cityscape or germanic fantasy Tolkein forest. It was westerns, admittedly treading the generic locales of movie westerns but fairly new to gaming. There was a joy to just rambling around the map. Hunting was a side-quest but it was more organic than most side missions, plus a new type of gameplay, and challenging when hunting legendary beasts. The story missions still suffered from compressing you back to linearity. Plus the standard GTA model of work-for-this-guy-for-awhile-now-kill-this-guy was in full effect. Not perfect but better.
Half-life 2 is still one of my all-time favourite games, and one of the only games I've played through multiple times. Hard to say why I think it's so good? Two things come to mind
1. It's linear but LOGICALLY linear, by which I mean you intuitively move in the direction the developers want you to. Nothing jars more than seeing what looks like an optional path or doorway, only to hit some barrier. In HL2 I found myself reacting to things and then releasing later than was the smart thing to do, and the only way to get through. The Early CoD games had the same forethought about player behaviour.
2. The organic variation in gameplay. You start off unarmed. Then you're running for your life. Then you've got a pistol and practically golden eye your way until the fan-boat. The fan-boat! Ravenswood scared the crap out of me. Tunnels, the coastal road and the car, the ant-lions thingies, Nova Prospekt, back to the city, town hall, then the spire fight. All this with balanced pacing between exposition, varying gunplay from battles to stealth, and sensible puzzles thrown in. And none of it requiring set-pieces or taking control away from me.
Of course it has some ridiculous logic in it. If you're a fan of Half-Life 2 then you MUST read "CONCERNED: THe half-life and death of Gordon Frohman" the best web-comic I've ever seen http://www.screencuisine.net/hlcomic/index.php?date=2005-05-01