Yeah, well, if you're tweaking in ResEdit, you might as well tweak the particle beam to take no fuel...and no, not everyone cheats. Sure, we might've done it before, but we learned, as you will eventually, that it just isn't quite as fun without the challenge.
But yes, I have to agree that secondaries just don't cut it sometimes. But I use them now because 1) I don't use the monty python tactic anymore, 2) it's more realistic, and 3) I'm figuring out ways to keep them useful. In dominating some outer Cofederate stellars, it's convenient to have 20-odd missiles and a few heavy rockets around to finish off a ship if it happens to slip out of primary range. And generally a takes a long while before I actually run out.
As far as secondaries go, I generally stick with two missile racks and one torpedo launcher. The torpedoes are helpful in chewing shields away, plus it keeps that realism factor in (I don't like making my ship a different ship, just with the same hull). And yes, they generally don't work with fighters, but when the fighter's on top of your ship, it works. It's fun to do with Defenders. And missiles are, well, missiles.
And don't forget about the javelin rocket -- it's arguably he best secondary weapon in the game. It's a powerful supplement to your guns, has a long range, and has enough impact to keep large groups of fighters at bay.
And most people don't realize how useful the heavy rocket is. It's a pretty nice weapon, providing you aim it right. Even considering weight, it does more damage than the torpedo.
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Mike Lee (Firebird)
I did it accidentally, actually, I was trying to do the Confederate mission string, then I sort of accidentally 'fired' (destroyed, yes :D) on a Confederate ship...Or maybe I just defected. In any case, then I worked for the Rebels and it was cool.