You have 8 power in your weapons system:

[IConquer]

And 3 weapon slots.

You are given a choice between two loadouts:
Burst laser II
Burst laser II
Glaive Beam

or

Heavy Ion I
Heavy Ion I
Glaive beam

Came upon this decision earlier... I've never been so conflicted. Both are so tempting.

[space_commie]

I like the 2 burst laser II better, might as well get in some incidental damage while knocking their shields down for the glaive beam follow-up.

[5thHorseman]

Burst Laser 2 is the single best weapon in the game.

Actually I would have considered 2 ions and 2 burst lasers

(no I wouldn't... You said 3 weapon slots)

[IConquer]

yeah, I ended up going for 2x burst laser II, but I had been using two heavy ions before I got a burst laser II and spotted one in the shop at the next jump. I was very torn.

[mqstout]

If I were heavy on boarding, I'd consider the ions.

[MoD1982]

Do ion weapons have an effect on Zoltan shielding? I can't recall... but either way my vote is for the burst laser setup. There's just something about lasers(and their lack of reliance on ammo) that I love!

[IConquer]

Do ion weapons have an effect on Zoltan shielding? I can't recall... but either way my vote is for the burst laser setup. There's just something about lasers(and their lack of reliance on ammo) that I love!

for every 1 point of damage the ion weapon deals, it will hit zoltan shielding for 2 damage.

An ion bomb, for example, subtracts 8 from the rebel flagship third stage total.

[Jerjare]

Yeah, there's even an event in Zoltan space where you witness Zoltan ships doing a training execersise and it makes mention of their Ion vulnerability. Ion II, in addition to being an excellent weapon anyway, is probably the most reliable way to tear down Zoltan shields.