I see lots of guys taking the axes/knife for melee plague marine.
however, it seems to me that a flails simply out perform 2 axes in any circumstances.
assuming you want to invest 20 points in melee weapon for you PM, and that ones field a 7 man squads:
With 2 flails, you will average 4 hit, where you are guaranty 8 hit with 4 axes.
Flails hit are ST 6 vs the axe ST 5, will make a big difference vs light infantry, may help with light vehicle but will not help you against most heavy infantry. Both are great if you planned to use Veteran of the long war and/or blade of putrefaction.
Both have the same -2 AP, as usual, good against any low armor target of invuln save target.
The axes will forces more armor roll, so more chances to get at least 1 through? however, both have the same amount of average wounds, with the flails having the better high roll of 12W. Since Flails wounds are carried over the D2 stat is never wasted.
so, for the same amount of point you get usually the same average damage with a chance for a high (and low) roll. on average roll, the flails always outperform or is equivalent to its point in axes. however, the most important point are the 2 marines that are "freed" from having an ax and can each add 2 knife attack or carry a bolter! they can act as ablative wounds for the unit or be given axes if you wish.
For me, unless you really hate d3 weapon, the flails seems like the oblivious choice until you maxed them out.
Note that this is all MatHammer theories, I look foward to see how it works out in game.