I'd say that one of the better ideas so far is one that hasn't been deeply explored: allow fighters to be constructed a la ships, albiet with only one hull point, no shields, and no hyperdrive.  They could also be given overthrusters as standard, perhaps?

1) Reduce the fighter's effectiveness

2) Re-introduce the Fighter Defence Network from the Compendium

3) Add an anti-fighter weapon enhancement or AFFC that allows vessels the ability to target fighters effectively.

What would you want tractor beam rules for?

Sure you have.  I think that is the true problem with the Stealth/LRS. Try a game without reverse (or with it limited to 1 hex/turn) and see if that makes the Stealth/LRS combo a lot more manageable. Even ships not designed to specifically counter that combo will be far more effective at it.

Honestly, I can't think of a single battle where I cried "stop moving backwards you bastard!"

And the SG/LRS combo was particularly cheesy when combined with inverted range modifiers.

The problem is that you can't close fast enough to kill the opponent's ships before you lose 20% of your CR to the needle guns.

I did better with:

Lots of fighters
PDS
Shields 2
Very Fast Ships (8+ speed)
Sunbursts (which I play very poorly)

Never did much with stutter drive, but that's one for the record.

1) Dogfighting. Is it something that is recommended to be used? Without it, there doesnt seem to be a way to really 'defend' against Fighters getting off their first attacks. With it, it seems like some of the Fighter customizations are weakened. Things like Bomber become very hard to use because an opposing Flight can just pin you forever until you are dead. Also, Drones and Marines seem a lot less appealing, again if they can just be pinned until destroyed. IMO Flights should have a chance to escape the Dogfight or somesuch.

2) PDS. How does this work? Do you make an extra PEN roll that fails on a 1/3/5? If its part of the 'normal' Pen rolls, doesnt that make the PDS a more or less cheaper alternative to shielding (and a good addition for certain shield classes)? I just dont see this thing as being 'balanced' across the board as its obviously FAR better for some shield numbers than others. Are we missing something?

3) Armored Gun Batteries. From what it appears, AGBs simply make your weapons cost 50% more (SUs and CR). If so, then why not just increase your number of weapons by 50% instead of using AGBs? AGBs increase 'life expectancy' of a weapon by an average of 33% (5+ save). Simply stuffing on more weapons increases it by 50%. Yes, it does add more Battery hits to the damage chart, but I would think that that is WELL worth it for 50% more firepower as well. I would think it really wouldnt be that effective to put AGBs on a ship unless it was under 33% cost. Either that or if it took up 50% of the SUs, but only 25% of the CR? Is there some other cost alteration that we are not seeing?

4) Stealth vs ECM: It appears that with the current FAQ ruling about Stealth and 'for better or worse',  that Stealth is only marginally better than ECM in many situations. Sure, it does prevent attacks at Long range, but beyond that, the effects are similar. Unfortunately, there are situations where Stealth is significantly worse than ECM (like with reversed Range mods or vs weapons with no Range mods). That makes them pretty much close in capability, but the Stealth system is larger and far more expensive CR-wise. As a suggestion, why not allow the Stealth Generator to always give the best modifier of the real or modified range. For example, if a Stealth Ship is in Short range of an inverted range weapon, it can keep the Short range rather than counting it as Medium (and being worse off than even not having the system at all, let alone ECM). An easy way to phrase it would be 'Ships with Stealth Generators always enjoy the more advantageous of either the true range or one range bracket farther out'.

5) Rate of Fire. Its been touched on before, but I haven't seen an 'official' response as to what to do (if anything). Its become evident to us that, by far, the most efficient weapon is always 3/1/1 + whatever specials. It takes up less space than 3 equivalent 1/1/1's and is definately more efficient than increasing Pen or Dmg at all. It also happens to be the best build against Fighters. To me, this is a potential major screw as the point differences between 3/1/1 ships and other weapon combos REALLY add up. Everything else even, a 3/1/1 ships will beat another ship with any other R/P/D combo (again, from what we can see). For ourselves, we agreed to limit the number of RoF increases on our ships, but its still an imperfect solution.

However, I think Noel meant the Fighter Defense Network, which acts in the fighter phase..

As far as I know, the KBE rules were specifically designed for the Wars of the B&K, and are not an integral part of VBAM.