Adding jump capable fighters are not necessary.
If your opponent has the exit point of his gravity well covered with a powerful defensive force, Phase Space capable strike craft could go in first. They would punch through the defenses, and force the enemy defenders to pursue...reducing the total enemy firepower covering the exit point. If the enemy doesn't bother to follow your Phase Space strike craft away from the exit point, you can then destroy all vulnerable installations/platforms at your leisure (including any Phase Space Inhibitors)...you can even jump deeper into the next enemy held gravity well and see how much damage can be done there. Most likely though, your opponent will try to deal with these advanced strike craft as soon as they show up.
First and foremost, what's the point of building a defense if it's useless against an attack? That player is doing the most logical thing; making it easier for the attacker to break through rewards the aggressor and not the defender.
Building flak frigates takes time, certainly not enough time if you have a wave of bombers directed at your factories. Should I have prepared first? Absolutely not, fighters are supposed to remain with their capital ships and not jump out in the first place! Why not add a flak turret? Because it's repetitive to add these things when you don't actually need fighters to be jump-capable at all!
You can break this defense by doing what you always do: jump in a larger fleet. Don't like the casualty rates? Then don't jump in and blockade his only
exit. He can only get so much resources if you've got half the galaxy under your hand. If it's not his only exit, jump in on his other entrances. Force him to split up his fleet. In chess, if the enemy king is surrounded by pawns, you can't expect the creators to give you a break and hand you micro-pieces to break through and dsetroy the pawns. You have to go in there, and you have to lose your units to get your objective. There's no reason for bomber and fighter wings to jump in if your capital ships can't do the job. They're not supposed to be your attack force!
This strategy you describe as sending in fighters and bombers en masse can be used for scout frigates as well. Why don't you just send 30 scout frigates in? Even if they're not effective, your capital ships don't take the brunt of the damage.
Phase Space capable strike craft would obviously be a lot faster and more maneuverable than capital ships or frigates. Therefore, they would make an ideal force for covering two (or more) key positions at once. They would also be able to reach a besieged ally more quickly than your capital ships or frigates could ever arrive.
You also have to remember the logistics behind fighters and bombers. They are not supposed to be an attacking force, only a supplement to turn the tide in some battles. Like I said, that's what scout frigates are for; they're not slow, and you can build a lot of them.
Besides, speed adds a factor to strategy. Do you help your ally? Or do you attack your opponent when he is weak? Which is more faster? Being to cover your mistakes (for example, having only one fleet, or spreading out your fleet too thin) is just wrong.
To further push the argument, I believe jump capable strike craft are a very practical and necessary convention for the tactical aspects of the game. They fill a very big hole in the offensive and defensive matrix that currently exists within the game. In short they serve as the "shock and awe" component for an aggressively postured player as well as a "minuteman" first line of defense for the conservatively oriented player.
I don't believe so. Like I said, what's the difference between an equal force of scout frigates? If you want a better defense, build more units and station them there. If you want a better offense, build more units.