Actually a balanced fleet has less problems than a pure Ka'Tan fleet.
As an example, i use a Bin'Tak, a G'Quan, 2 Rothans, and from now on 4 Ka'Tans in that fleet.
Means i have two ships to move, that dont need to boresight. First turn the Ka'Tans prolly wont be able to fire anyway. And later on i can sacrifice the G'Quan during movement phase. It can take alot of damage, and the beam isnt all that much. Plus when you have Ship breakers loaded, i tend to go for APTE as well.
Ripple you are right, boresighting is a huge pain. Made my friend lose a game EA vs Vorlons, only cause i had enough destroyers on my side, to keep him from boresighting. Blammo heavy cruiser untouched.
OTOH Narn vs EA plays quite different. You have to give up ships anyway, it only depends on which ships you move first. Sometimes i dont care which ships in my Bin'Taks boresight, i just shoot the next best one.
But it does give quite an advantage to non-boresight fleets. Normally balanced by smaller numbers. But when you can reach those splendid 90 degrees, all of the sudden APTE (Tertius) or CAF (Primus) become all that more interesting, and not things with a huge cost added, also even if the 2 AD beam on the Octs aft seems puny, anything that gets into that acr is gonna feel it anyway. APTE a Bin'Tak, and lose the 6 AD beam?? Worth it, rarely. 4 AD aft, surely lovely, used not so often. Unless you get lucky with Come abouts.
Boresighting is rather nicely balanced, only when fleets start to lean on it too heavily, does it become a problem. And scouts, im not so fond of them, 5+ for redirect? Bleehh, Vree gave it good. Shadows too. Even Centauri get crazy with corvans, as ini sinks, and free scout thrown in. Any other i dont know about.