I think plenty of posts and people are in agreement that the end-game operations/flashpoints favour ranged dps A LOT and you immediately alienate a large group of players in a guild in order to achieve success on the hardest modes.
There are many simple solutions that can be done to balance this out and without wanting to search through lots and lots of posts 2 basic solutions are to add extra damage dealt to ranged players and extra bonus damage provided to melee players.
Simple Aura controls would help that, where being inside that range gives you +damage and outside could take damage away or give some negative effects.
I really hope something is being done about this as for end-game raids this has already become a big issue very quickly.
I dont think that adding +damage aura for melee could fix that encounter design flaws - it really just creates another one.
One way around this is like you said adding some kind ranged damage, forcing most of the players (including healers) to stick in melee zone and only a few (like 3 or 4) needing to stand at range to take some kind of voidzones/projectiles/whatever spam that prefer ranged targets.
Another way is to just fix the fights like Soa so he creates mindtraps inside a melee zone or not far from the boss, cause running all the way on the other end of the platform to kill mindtrap and then running back is plain stupid when you can stack ranged classes and do the fight 10 times easier (and yeah, some melee classes can force leap or sprint, but still).
And the Bonethrasher... I can't even think of way to make it melee-friendly without reworking either the fight itself or the UI so that players can actually run away from the player targeted by the boss.