I would like for this to be a thread of ideas on how to best play this mission, but also a small vent/education to those who are not coming into the mission prepared (You know who you are). Please please please make sure you come in with heals. Your ship is going to get destroyed at least once and it is going to have energy weapon or projectile malfunctions. When this happens your ship does not function to its full potential and you are hurting the team. Please make sure you come in with minor, major and critical components. Also, that you have hazzard emitters for the plasma that will constantly be put on your ship and will destroy your ship if the hull is already weakened. Also, have brace for impact equipped. It will help when the plasma torpedo spread is coming at you. Make sure to hit it immediately as soon as you see them coming. There is a bug and when they get close the game will go ahead and destroy you before the torps even explode.
Now onto the strategy. What I have found to work best is this:
You have 2 powerful cruisers and 3 escort class ships (or any ship with cannons that is pretty maneuverable). In the beginning take out the spheres as to prevent them from draining your shields. Next take out one or two cubes at a time. No more than 2 though so they do not overwhelm the team. After the first line is defeated and the Vger ships show up start on the left side where it is more maneverable for your ships. 2 of the smaller more maneuverable ships take the ends and kill the bolts and the probes. The other smaller ship stays in the middle and takes out anything that gets by so that it does not hit the cruisers. Cruisers focus fire on the Vger ship. If there are no probes the smaller ships should fire on the vger ship as well.
All ships should be moving and at a pretty good distance from the ship. If you are a target you should be a moving one . I have been on teams and lead a couple of teams where this strategy was very effective.
If you are pugging you may not end up with this exact setup, but the idea is that the smaller ships that are escorts and tend to do more DPS can take out the probes and bolts faster and can chase after the probes that might get on the otherside of the ship faster than a cruiser. The cruisers can withstand more so they can tank what the Vger ship is throwing at them.
As for the Queen's ship keep as much distance as you can between you and her and throw everything you have at her.
As a side note. For those in assault cruisers with metreon gas. The gas can be very effective against the Vger and Queen ship if you plan it right. The hull of the ship should be exposed for maximum effect.
These are just my thoughts and observation. I am sure there are other strategies that have worked and I would love to read them here. This is what the thread is for so please share your thoughts.