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I wonder whether 2 Ion Blast IIs will keep the Flagship's shields ionized through its cloak, I don't feel like doing the math at the moment. Maybe later. (My gut says it will, easily.)
You could also ionize whichever system your heart desires with the second Ion blast once shields are down.
Two Ion Blast II is pretty good and even allows you to stack ion damage. For a number of reasons, it's not quite as good as the 3 power Ion Blast II, but it costs one less power, so is arguably more energy efficient (while taking an extra slot).
It's a really nice combination with a beam weapon.
In fact, one of the better starting weapons combinations is the Zoltan ship that starts with two Ion Blast Is and a Pike Beam.
Everybody just keeps posting what weapons, shields and engines they have, like that is only thing that beats game.
It's very possible to take it out with default weapons and Level 3 hacking, although admitedly painful. Personally I would always recomend ion blast 1 and 2 together instead of the excess of having two, mostly because the big reactor requirment means you can't use it to hold you over until about sector 6, although conversely, you can easily make enough scrap to make up for skimped reactor/engines by going out of your way to fight in the last sectors and the last stand itself if you do purchase that kind of firepower.
Although that is a rule of thumb, and for the rock ship I actually would take it, since you can probbably keep one of them in the hold and then sell off some of the default equipment later when you're ready to transition to ion blast godhood, or if you accidently get to a point where you can survive attacks well but can't hit through enemies - at which point the rock plating is kind of a luxury anyway.
I found that once you down the shields (even 4 shields), you can have 1 ion on shields and 1 ion on something else and the shields will be down indefinitely so long as you don't miss. Phase 1+2+3 of flagship had no shields except when cloaking / super shield, so it will pretty easy.
Here I started a thread about a ship like that.
I have it saved too, at the last stand. If you want the continue.sav file, I can send it to you. It's a really fun ship to use against the flag ship ^_^
Edit:
Basically, I love 2 ion blast 2 guns, if you can get the scrap to update weapons that far, and have something to attack with (beam drone works great, burst 2 also works, or pike beam - also a really good choice)
Main challenge when dealing with Flagship phase 1 is that it is no slouch with evasion and has level 3 cloaking, which will intermittently give it a chance to restore its shields.