I've replayed both GoldenEye and PD on Switch Online and GoldenEye is the better (single-player) game. The crucial difference is that GoldenEye's levels don't take too long to complete, so on higher difficulties, the lack of checkpoints don't matter too much as you're only ever, let's say, around ten minutes at most from catching back up to where you died. The objectives are simple but often designed so you can pursue them in any order, or simultaneously: this makes it feel as though you're able to make choices and if one route isn't working for you, there's often another one to try. There are, of course, linear levels like Silo, but rather than feeling constrictive, these offer alternatives and force you to play differently. Silo is the most straightforward of the lot, but among the others, there are usually a few alternative paths to try, even if your progress is more tightly controlled by the designer. It gives the game a huge amount of replayability and encourages the player to mix up their playing style: stealth results in fewer confrontations, but playing (intelligently) on the offensive can lure guards into opening locked doors or from around corners where you might otherwise be ambushed.
The balance is a thing of beauty and it trusts the player to find these things out for themselves: my favourite example is Bunker II, where you start the level unarmed and can only pick up loud weapons (with the exception of some throwing knives, whose inaccuracy makes them pretty useless) until late on, which will bring masses of enemies down on you in a second. However, an unwritten rule is that single shots are much quieter than automatic fire, so once you work this out, it's a game of sneaking through the level, taking out enemies with controlled headshots until you've built up enough ammo to hold your own - there's also an exploit with guards never shooting through windows, which upsets the balance a bit but only tipping a difficult level slightly more in the player's favour. The fact you visited the level earlier in the game (albeit in semi-constructed form) also helps the player in a subtle way, offering a few new areas but meaning you go in with some existing navigational knowledge. It's really tense and enjoyable, and once again crucially a pretty short stage so restarting isn't a big deal. While there are a couple of duds (Archives tries the same trick as Bunker II but far less successfully IMO, while Control is a bit too long and difficult for its own good, and Cradle is a bit one-note and with guards who are irritatingly numerous, accurate and high on health), for the most part the game wonderfully balances its systems and level design to challenge the player while also giving plenty of scope for improvisation.
Perfect Dark first four levels represent the game at its best, even if all bar Villa (the best level by far) are far more linear. Unfortunately later levels dial up the complexity, introduce insta-fail conditions on objectives (Chicago is ruined by these agents who can call end your game if you don't kill them quickly enough), increase the linearity and take much longer to complete, meaning it's far more frustrating to have to restart after death. Stuff like invisible enemies - admittedly the game gives you a means to track them, which is a nice touch but doesn't fully alleviate how annoying they are - just feels cheap, and the larger levels means it's much easier to get lost. Rare had entered the phase of their N64 development when it felt like they were more interested in seeing how hard they could push the hardware than design thoughtfully and with precision: Banjo-Tooie and DK64 are the most famous examples of this, but PD also foregoes a lot of the care which made its predecessor great in favour of being a great technical achievement (which it absolutely is for N64 hardware). Unlike GoldenEye, it's a game which really needs checkpoints but doesn't have them, and while there's a lot about PD I love and wish were still a part of modern gaming - the per-level design variation for each difficulty level, for instance - it ironically shows its age by being closer to modern, story-led gaming than GE (which largely stands as its own fusion between immersive sim and full action FPS) yet without a lot of the conveniences which have become the expected standard. I've been waiting a quarter of a century for an excuse to call someone a 'flawed device', though, so it certainly has its moments.