Interestingly, we have a real split of opinion. Some people love it as it stands, some feel it needs curbing. In such a situation I feel that the only solution is to suggest an officially sanctioned alternative and let people choose.
My feeling is that a run of three phases is not excessive. By definition, a minimum of four of the D6 rolled in the first two phases must have been 6's, so those phases were relatively limited. The design intention of the multiple phases is that you do have a great opportunity, but that is at a relatively restricted point. You are certainly highly unlikely to be moving your whole force with just three Command Dice.
Based on the above, I suggested to a friend that after two phases where he rolled double 6, he then swapped one of his Command dice for a 'red dice', as per the 1940 Handbook. So that only counts for 1234 and we ignore 5 and 6. The player then continues to roll his hand with the red dice until he stops getting the next phase. At the point he reverts to his normal hand of five identical dice.
Some people have suggested that dice are simply removed from the hand. I'm not keen on that as I feel that is too much. Others have suggested that additional 'red dice' are added for subsequent rolls. Personally I think a little gut touch is sufficient. The chances of another phase drops significantly with just one red dice, but you can, of course, vary that as you wish.
I should state that I am personally happy with the dice as they stand but it's all about personal preference.
If you do try this method, I'd be interested in feedback.
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John