Soma: Story, Atmosphere, Thought Provoking
Deus Ex HR: Story, Atmosphere, Thought Provoking
BioShock 1: Story, Thought Provoking
DragonAge 1,3 / MassEffect 1,2,3: Story, Characters
Witcher 3: Story, Characters
Portal 2: Story, Mechanics
Undertale: Story, Mechanics
Alien Isolation: Story, Atmosphere, Mechanics
Mirror's Edge: Mechanics
Braid: Mechanics
Dark Souls / Bloodborne: Mechanics? (Haven't played)
Blood Dragon: 1980s simulator
I can identify the "commercialization" trend that you're talking about if and only if I focus my attention to a single franchise or a single aspect of a single franchise. Example: Mass Effect lost its hard SF edge in 2, 3 but the characters and mechanics got better. Starcraft lost its story and character edge in 2, but the mechanics got better. Bioshock lost its philosophical depth in Infinite but the story and characters got better.
Overlaid on top of this is a trend of increasing production value. Every franchise gives you some facet to point at and say "devs don't care about X, only production value, boo." This ignores the boring explanation that it's hard to churn out sequels that exceed the original in each and every possible point of comparison. Sequels need to be evaluated on their own merits and the industry needs to be judged as a whole. Otherwise everything is guaranteed to look like it's going downhill.
Or maybe I'm wrong. Let me know your favorites and I'll promise to give at least one a try.