Even in an individual sport* head to head matchups can be misleading, but the 4-2 record is absolute BS, since Shaq was in his prime and dominant on 3 of those Lakers teams. Without Shaq, Kobe-led teams often lost too early (or missed the playoffs completely) so they never could get smoked by San Antonio (which happened in 2013).
Duncan's peak was lower than both Shaq and Kobe, but his career was better. More wins, more rings, more playoff appearances, more playoff series wins, more MVPs, and more Finals MVPs.
They both have 5 rings.
Kobe was gone with his torn Achilles for the 2013 playoff match up.
If you are penalizing Kobe for having Shaq, you should penalize Duncan for having Pop and only directly compare them when they each had an all time top 3 all time coach leading their team. Kobe w/ Phil was 4-1 in the Playoffs against Duncan w/ Pop only losing, largely because Shaq was fat, in 2003. Further, in Phil's 11 seasons, Kobe wen to 7 finals and won five titles, Duncan only went further than Kobe twice in those 11 years and won two titles in two finals appearances.
In terms of washing out early and keeping them from meeting each other, it happened both ways:
Seasons where they did not meet in the playoffs, but both teams were in it:
2012 - Lakers (under Mike Brown) out in the 2nd round, Spurs made it to the conference finals
2011 - Spurs washout in the first round as a 1 seed, Lakers lose to Dirk's title team
2010 - Spurs washout in the second round, while the Lakers win the title
2009 - Spurs washout in the first round, while the Lakers win the title
2007 - Lakers washout in the first round, while the Spurs win the title
2006 - Lakers washout in the first round, while Spurs lose as a 1 seed in the second round
2001 - Spurs washout in the first round, Lakers win the title
2000 - Spurs washout in the first round, Lakers win the title
Duncan was certainly more durable than Kobe, Kobe didn't finish the 05, 13,14 or 15 seasons. Duncan was also a much better team player and less of a coach killer than Kobe, managing to keep his great teams together and keep Pop with him for his entire career. But Duncan's peak was nowhere near as great as Kobe's, and in their prime, with both led by top coaches Kobe's teams dominated Duncan's. They are both somewhere between the top 5-10 all time, but choosing between them is really a matter of picking between a better peak or a better total resume. It will be cool to see them go into the HoF together, though Kobe will certainly care more about having to share the attention.