This idea came about from brainstorming on the Demigod IRC channel.
The basic idea was to link flags in the same path like nodes from Unreal Tournament. The result would be that in order to take a flag in the enemy base, a team would need all the neutral flags between the bases in the same line as the flag they want. To use the current map as an example, to take the enemy's Valor flag, you must control the middle experiance flag as it is in the same path as the valor flags.
An argument against it was that it could destroy some strategy in Demigod(Ryo2810)
Also, it was suggested that instead of blocking capture, not having a link to a flag would increase its capture time(Evangel)
Taking all that into account, my idea for linked flags is to have three diferent options for it in the game setup screen.
None - no linked flags, this is for those that don't like the idea
Block - this makes flags uncaptureable unless you have a link to them
Time - this increases the time it takes to capture an unliked flag. This could have several multipliers to select from, such as Time 1.5x, Time 2x, Time 3x, etc