And HL was praised because it changed the formula and went for a linear level design that actually looked like real life buildings instead of labyrinths that only made sense as videogame levels
The issue is that HL1's design approach is a narrow corridor where all the doors are fake. It looks like a real building, sure. GoldenEye's approach was to create an actual building where the doors worked. Which one is better is a deep design schism, sure, but HL1 was pretending to be something GoldenEye actually was. HL1, and HL2 alike, were throwbacks to "painted corridor" level design that the architecturally conscious GoldenEye had already blown away. In terms of actual level design, Half-Life plays like a game made by someone who was a fan of Quake II, but wanted it to look more realistic.
(also, big focus on storytelling while most FPS were like "kill bad guys, save world").
Which, again, GoldenEye had already done. The only real difference was that HL1 was seamless. A significant difference, sure, but one straight from Quake II.
For some reason, Half-Life 1 gets a lot of praise for scripted events occuring around the player, but GoldenEye did this a year earlier. Scenes from the film were recreated as NPCs engaging with the player. NPCs talked to Bond, Bond talked back to them. The designers even took pains to recreate iconic scenes from the film such as the train escape set piece without resorting to cutscenes. Every important story moment occurred through Bond's eyes.
Whether people like it the most on N64 isn't even my point, I don't think it's possible for it to claim the title of "best shooter of all time" when things like Quake and DOOM exist.
The problem is that people who are fans of GoldenEye (I'm a fan of PD, not so much GE) see games like Doom and Quake as extremely primitive and crude and fundamentally less worthwhile gaming experiences. The problem is that this is ALL opinion. "Good" game design is pure opinion. You may as well argue whether Call of Duty: Ghosts or Soldier of Fortune II are better games.