[Taera]

Yes i've encountered the problem with fleet leader being destroyed and/or damaged and have found several ways to evade this problem.

First and most important is to use correct formations. Several ones, such as the Flying V and Arrowhead are quite useless as my personal expirience shows. Those useful are the ones that hold the leader in the middle (i use Turbine--my fav, Butterfly and Spider, all in appropiate situations) because then the formation spins around putting each time a different ship under enemy's fire, plus putting each ship under PDC protection while half of the ships are away from the enemy fire at time.

Second the leader should be well protected by armor and shields, do not put your weakest ship as fleet leader.

Third is the wise selection of fleet leader.
Remeber the Targeting Options. If its a leader-in-center formation the leader will never be closest/farest. YOu can make it wouldnt be most powerful/least powerful. etc. By using this the leader can avoid enemy fire for quite a while.

Also i have to say i never used the custom formations from TDM because i feel they would give me a major edge over the AI. Some formations such as the Barrage are awesome, good job for the TDM staff.