The best solution may be that we need to pick and mix different ideas.
With the Flag PvP...
If you flag to PvP, there is higher level range for attacks (for and against you), drop more cash upon death from PvP (maybe 20%)
If you flag non-PvP, there is a lower level range for attacks (for and against you), drop less cash from death with PvP (10%).
There can be a 24-hour delay between changing your status on PvP.
Completly remove protection in w3, higher range in w2, lower range in w1 and small to 0 range in w0.
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The best way to work bases and probably the whole PvP system IMO, would be using the Team Level system, and it would even the score with low-level base alts.
If a low level in a high level team cannot handle it, then it is the teams problem to do their duty as good team-mates and help him manage with better gear, skills etc. or let him go level for a while in a team around his level.
Hmm...