I stopped using X-weapons when I couldn't beat an awoken empire with my fleet which was two times smaller than the fleet of the enemy. Instead, I focused on plasma and disruptors and wrecked the bastards with very few casualties.
X-slot weapons seem very powerful on paper but, in practice, I've found them to be quite weak especially if the fleets are large enough. Once they start mixing up, all x-weapons become useless, but you still have to output a lot of damage points to win. Idk, at this time, I'm entirely unconvinced that they can be useful in any way.
First, are you saying you lost to an awaken fleet that was 2x larger than your own, and that's why X weapons are terrible?
Anyway, what kind of FE was it? Xenophobic have lots of kinetic artillery and Cruiser computers (which increase fire rate and have the ships rush in to the fight) w/afterburners on all their ships. They are pretty much designed to counter a Battleship-Cruiser heavy comp, especially one that expects to sit back and snip with X weapons all through the fight.
A X-weapon Battleship/ Cruiser heavy settup, on the other hand, would wreck a Spiritualist one six ways from Sunday, thanks to their dependence on arc emitters, torps and missiles.