Point defense does have to be nerfed significantly... Stock PD is an impenetrable wall.
Note: Just to be clear - Point Defense is comprised of Fighters, missiles, fighters and more fighters
An unopposed fighter screen should shoot down 95% of what the enemy capital ships can throw at you.
The way I see it working is the following:
A first wave of fast fighters from both sides will meet, and start duking it out.
The bombers will tend to be slower, and by the time they get through the skirmish zone your second wave of interceptors should be gunning for them. If they fail, and the bombers get in range, your capital ships will certainly take critical damage.
The capital ships could take down a few bombers with anti-fighter missiles, and should also be able to shoot down a few of the bombers' missiles with their own anti-missiles, but not many. Any remaining close-in fighter screens will have a small window of opportunity to shoot down the missiles as well, after which it is down to how much armor you have.
Once the bombers are spent, the remaining fighters will continue to dogfight and the capital ships will lob supporting missile fire into the fray.
When one side gains an advantage, their fighters may press on to strafe the hopefully crippled enemy capital ships.
The small fighter guns will certainly be much less effective than the bombers, and the missile fire will slowly whittle down the fighters, but they will keep shooting until the battle is over.
Your 50-200kt support ships should be positioned to protect your big expensive carriers as long as possible, but once your fighters are gone, you're in deep trouble.
Small numbers of fighters getting past the main lines are not too much of a threat.
Assuming the ships have good strategies, a group or two of fighters sneaking in will quickly find a pack of missiles locked on.
Missiles are most effective against small numbers of large stacks, so these situations are advantageous to the defender. The capital ships are shooting different enemies than the fighters are, and there is less wasted ordnance.
---
Allowing ship-to-ship weaponry to target fighters as well is reasonable, but the accuracy should be pitiful. Only the smallest guns would have much chance beyond the 1% minimum.
It is the carrier battles mod, and fighters should be the primary weapons and defenses in combat
.
Once your fighters have been defeated in space, your capital ships are all but lost.