I think it really depends on what you interpret levels to mean.
This is how I feel, too. Different games treat levels differently, especially first level. Crafty Games appears to allow first level characters to be fairly competent compared to some of the other systems I've played.
So, I would say the agents that demonstrate a high level of skill across a large range of abilities are higher level, but otherwise they can be adequately described by low level characters.
For instance, Ethan Hunt (Mission Impossible): High level. He can do everything. The rest of his team: Low level. They do whatever their specialty is and very little else.
This sounds like specialists are always extras, which seems kind of counterintuitive in a class based game, especially
when there are Expert and Master classes that emphasize specializing.
Sam Fisher (Splinter Cell): Low level, he only does stealth (although he is exceptionally well geared).
Solid Snake (Metal Gear): Low level, he also only does stealth (boss fights notwithstanding).
For video game characters that don't significantly change/improve in ability in game
(such as the characters you mention, who only really improve the gear they are carrying), I'd say that "leveling" is a matter of player
skill rather than character
skill. Someone familiar with the games will know when and where to use the abilities to better effect than someone unfamiliar with the games.
Desertpuma mentioned the first year of various shows. I think I would be even more limiting. As a blanket statement, I would look at the pilot episodes of shows for ideas of where I feel "Level 1" would be. The characters are typically competent, if a bit inexperienced (either in their abilities or working with a team of similarly able professionals). By even the midpoint in a season, the characters have already developed and expanded a bit. Part of this might be due to the nature of television programming, which is understandably different from RPGs.
Something else to consider (as this is from Crafty Games) is the use of Campaign Qualities and their potential impact on player expectations. I can't see why any of the aforementioned ideas couldn't work with an appropriate set of Campaign Qualities.
What should a Level 1 Super Spy be able to pull off? First, Super Spy to me means somebody who can do everything (with the possible exception of creating gear and maybe
hacking), and do it well. tfwfh's mention of Ethan Hunt fits the bill. He can drive, shoot, impersonate, sneak, lead, etc. In fact, the list of things he can't
do (and do well) is probably smaller. Alias' Sydney Bristow is in a similar camp; she does everything but monitor video feeds and make gear. Personally, I don't think the Super Spy is necessarily appropriate for an RPG. In the cases of Ethan Hunt or Sydney Bristow, they are lone wolves with a support team (read: extras). I like the idea that multiple people can participate and are needed at the same time
for an operation to succeed. What I imagine is more along the lines of Leverage or the TV series Mission: Impossible than Alias or the movie version of Mission: Impossible.
Perhaps I need to look at the idea of a Super Spy differently. Maybe the Super Spy is exceptional in one category or focus and "merely good" at all others? That way they can still be part of a team? I'm trying to come up with an example, but I'm drawing blanks...