It all boils down to how you play the game.
If you like having a large, heavily shielded ship with lots of guns and secondaries, then go with the Igadzra. Their Igazra ship is by far the best "heavy battleship" in the game (IMO). The problem with the Iggies is that their technology really leaves something to be desired. The plasma siphon has its uses, but there are better secondaries. The SAE modules are just like the SAD's... they suck. Can't hit anything. Still, I like going with the Iggies so I can fly in my Igazra. I just ditch all the secondaries and get a Crescent Fighter Bay. it serves its purpose, and I've "beaten" the game many times by siding with the Iggies and using the Igazra.
The Zidagar.... well, I don't really like them. I think their mission string is the most fun/entertaining, but overall, I think the other strands are better. The Zidagar have a rather weak gövt ship. Lots of people like the Zidara, but I don't. The phase beamer is a waste of space (space that can't be had back) because as a weapon, it kinda sucks, and added to that, the low amount of fuel gives you little time to use it. The only reason I'd go with the Zidagar is to get that free 20 tons of space. That can come in VERY handy on any vessel. The ECM system is nice, but secondaries don't hit anything in 1.0.2 anyway, so what does it matter?
The Aggies have the best technology in the game. The shield enhancers can make certain ships damn near invincible... which is a nice quality to have in the game. But, then again.... I have the need for big ships and lots of guns and turrets. The Aggies have a nice gövt ship, but you can't buy it, which really sucks. You could steal one early on, before you side with any strands, but then you'll have to work harder to get your rating with them back up. But, once again.... for me, the shield tech is rather useless... the ships I use hardly see the difference in shield regeneration time. Plus, the aggies have a rather boring mission string.
So, there's my 2 cents.
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