Those are all in-story differences, though. If you compare a PC street samurai with an Ares Alpha and Wired Reflexes 3 to an NPC street samurai with the same, they're virtually identical.
But focusing purely on "in-story" factors won't tell you whether or not the game has an agenda of the sort being discussed here, and what its agenda is.
I don't know Shadowrun except by barest of reputation, so I'll use Marvel Heroic RP as my example.
In that game, the Black Widow (just to pick an example) can be played as either a PC hero or a NPC villain.
If she is played as a hero, then when building her dice pools she will get a d6, d8 or d10 depending on who else she is hanging out with (unsurprisingly, being a supers game, MHRP's resolution mechanics pay attention to the composition of teams),
If being played as an NPC, there is an option to keep those same dice, or - if she is intended to be a secondary character - to step them down, to d4, d6 and d8.
As a PC, certain abilities are activated by the player spending a token from a limited but replenishing pool. (The token are called "plot points". In D&D terms they straddle the roles of both action/fate points - ie metagame tokens - and spell/psionic points - ie heroic reserves that the character can draw upon.)
When the Black Widow is an NPC, those same abilities are activated by removing dice from the Doom Pool, which is the GM's resource bank.
If the Black Widow wants to acquire cool guns or tech, a check is required that involves building and resolving these dice pools, potentially spending these resources, etc. The overall mechanics of the game are set up so that as thse checks are made there is an ebb-and-flow between player plot points and GM's doom pool, but the economy slightly flavours the players (and hence the PCs).
There is no in-fiction difference between the Black Widow as a PC or an NPC - she could change statuses in the course of a scenario, for instance - but the game still has a strong agenda of PCs-as-protagonists. Black Widow with a cool gun as a PC is, in the fiction, no different from Black Widow with a cool gun as an NPC. But the mechanics for acquiring that gun, and of what she might do with that gun, favour PC protagonism.
As I said, I'm not familiar with Shadowrun's system, but I took [MENTION=336]D'karr[/MENTION]'s point to be that the PC build rules that the players are using, compared to the NPC build rules and scenario design rules that the GM is using, produce an outcome that supports (fairy strongly) the protagonist status of the PCs.