I agree on the area defense issues, I don't think I have ever used it effectively in a game.
The reduced missile speeds should help on this but I don't think its going to go far enough. Generally I'd expect area defence to be useful where you can detach escorts from you main TF and have them usefully engage incoming missiles before the reach the main group. I wonder if missiles passing through an engagement envelope being fired on rather than just those that land in the engagement range would help.
Not such a fan of the tracking bonus applying to range unless this is also applied to ship to ship combat.
I think 'passing through' would probably be the best implementation of area defence. That wouldn't be too hard to implement and I could use the closest point of approach during the increment.
The main problem is tactical utility though rather than mechanics. If a ship is deployed away from the main force it becomes an easier target so the benefit of enhanced energy point defence is countered by increased vulnerability. The only way the area mode really gains over final defensive fire is if it can fire more than once, which means long-ranged turreted weapons with appropriate fire control. In that case, even though it might fire more than once, a ship designed for final defensive fire has more weapons for the same cost, so firing more than once doesn't necessarily help. Maybe some sort of 'stealth picket' could help, but again cost vs capability might still not be viable.
Rather than than trying to make area mode work for energy weapons, maybe we just have to accept the concept isn't really viable. Even in modern warfare, the 'Anti-Air Picket' would be armed with AMMs rather than short-range weapons. A forward AMM picket really could make a difference.
Re tracking bonus: If energy point defence does prove too effective with the new changes, I would probably remove the tracking bonus altogether.