Hold up. I'm apparently one of the only people on earth who enjoyed reading TTON, but I felt like there was lots of little choice and consequence (which dropped off substantially after the first hub), but very little that was meaningful except for the end. The whole thing was like a loosely tied together series of vignettes--lots of choice, not much consequence. Did picking your favorite color really change anything? I don't have the wherewithal to read a million words again in order to find out.
Elex vacillated between moments of great C&C and being totally on rails--it was a lot more reactive in the early game. I did like how they locked you into the various endings based on your behavior/elex potion abuse. But I guess I can't think of anything better from the last year, which is what PB should put on the back of the box.
The tides and cold systems were poorly implemented. They both facilitated different endings, though Elex was more simplistic about it. In numanuma, having a blue/silver tide enabled a rejoining with the spectre to 'become whole', while jumping through a bunch of hoops (with a red tide? I didn't do this) allowed you to become the new memovira. These choices were divorced from the endgame dialogue with the sorrow, which meant you could see many different slide combinations. The ultimate result is not a huge gap, but it's there.
Things start pulling apart with regards to companions. In Elex, your companion reactivity is largely binary; you kill Duras or spare him, you fuck Caja or Nasty, you save Ray or...you don't? I know he can survive the end but this appears to again be based on cold level and not his quest. Falk is a one-noter, though perhaps taking him to kill his 'dad' triggers something. Arx is the only apparent exception here; you can kill him, dine with him enthusiastically, or find him a heart to compromise. The second option
may lead back to the first. I admittedly need 5 more playthroughs before confirmation can be given.
In contrast, Rhin alone has 5 different fates. She can be sold into slavery at sagus, sent through the orphan portal, sold to the decanter, sent through the weird dude's portal to return as an adult, or simply kept along for the ride (OP option). Erritis can be sacrificed for raw power, left uncured, or cured. Matkina can be sacrificed, become the new leader of miel avest, or the new memovira. Tybir can be abandoned in sagus, or has a few different endings based on his quest. Callistege and Aligern are similar sans abandonment. I don't know about the toy because lul fuck playing that trash again just for slides.
You're right that sagus held most of the tangible c&c, but even that section alone consists of more than the bulk of Elex. Many sagus quests have several solutions compared to Elex's often binary approach, but neither game does a good job of providing long-term consequences outside the slides. Elex's domed city is the only area where your choices actually matter, but it is again completely binary and shallow. The one area Elex beats numanuma in c&c is post-game faction killing spree, because the latter doesn't feature anything comparable. Elex is a much better game overall, but numanuma's reactivity was superior, to the detriment of everything else it seems.
tl;dr Where numanuma's c&c fails, so too does Elex, but in many parts it is better. Whether by a nose or a mile, a win is a win. Elex is still my goty though because it's actually playable.