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I noticed that with very few rare exceptions upgrading your weapon to higher "MK" version is actually a downgrade.
You can operate multiple lower level weapons with the amount of power just the one upgraded weapon takes. And if system power is cut by even 1 point then a 4 point weapon is shut down, not so with multiple lower point weapons.
Not to mention direct downgrades like the fact the pike beam 2 has double the damage but half the distance so it hits half as many rooms and does the same amount of damage total.
And higher level weapons take longer to charge... shooting first and taking out the enemy weapons is one of the keys to victory!
Not to mention shields stop "hits" not "damage" so multiple weapons are better there too.

So basically, high end weapons suck.
Isn't that kind of the point? That you are meant to make choices. A risk-return tradeoff?
Yeah, you need to stop thinking in terms of upgrades. In this game, the weapons are all designed to be balanced against each other. There is no such thing as upgrading your weapons, just finding ones to fit more situations.
1. There is no choice, the "upgrade" is inferior 90% of the time.
2. The heck there isn't upgrading. Not all weapons are equal.. many weapons suck, some are awesome. Replacing a crummy weapon with a good one is an improvement.
3. It is not me who is "thinking in terms of upgrades". its the game explicitly calling certain weapons and drones an upgraded version.
For example: "Burst Laser II: Slightly improved version of the Burst Laser that fires more shots per charge"
Is the default weapon on the kestrel and the above is a verbatim quote from the game.
It has an incremented number, and it claims to be an upgrade... A lot of weapons and drones claim to be upgrades. So don't give me the "there are no upgrades" nonsense.

Now, this is an unusual case because Burst Laser II is the best weapon I have come across yet. 4 of those will shred anything, including final boss. (or 2 or 3 of those coupled with ion weapons mmm mm)

While it is better to have 2x Burst Laser I (1 power each, 2 shots each doing 1 damage per shot, faster recharge) then it is to have a single Burst Laser II (2 power each, 3 shots each doing 1 damage each, slower recharge) the Burst Laser II is actually a viable weapon because it takes 2 energy and the Burst Laser I suffers from the fact that you are limited to only 4 weapons per ship.

The Burst Laser III on the other hand fires 4 shots but for 4 energy and has an even LONGER recharge rate. Completely non viable as a weapon since the absolute max weapon energy you can have is 8. And on a decent ship that will be coupled with 4 weapon slots.

The biggest issue is that shields recharge in about 1 second while a weapon in about 10, and with dodge its going to be tough to break enemy shields. This makes pikes like weapons useless as well as heavy lasers. Missles on the other hand are too hard to come by so an arsenal of missiles is not a viable strategy as you will run out of weapons in a snap.
So you must somehow breakdown enemy shields in a single volley and that means many shots.

Heavy laser II for example goes from 1 shot 1 energy to 2 shots 3 energy (non viable, too much energy) and of course longer charge duration...

Basically:
With the exception of Burst Laser I to II case (where lack of hard-points make II a better choice despite 1 being the superior weapon), all other upgrades come with such obscene drawbacks (power cost, charge rate, shot count per energy unit) that it is better to use the non upgraded version
Post edited September 16, 2012 by taltamir
Sorry, but I simply don't agree with you. Except for Burst Lasers being awesome, because of course they are.
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taltamir: Not to mention direct downgrades like the fact the pike beam 2 has double the damage but half the distance so it hits half as many rooms and does the same amount of damage total.
There's a pike beam mk 2?
I tend to agree with the OP. You need at least some rapid fire weapons the breach shields. After you get through shields, though, all the other stuff becomes useful too. You just need to be able to fire volleys of at least 4 shots right before using anything else.

I wonder if a weaponless boarding party based build is workable.
Generally, the ships you unlock tend to get more powerful. Especially the layouts. And layout B of the Kestrel ship had surprised me by following this OP's theory : it's got 4 tiny lasers.

Now one should also consider that you have only 4 weapon slots, so, 4x1 is still waeker than 4x3 weapon power.

And one system you sometimes find allows you to pre-heat weapons. To fire directly at arrival. In this case, your slow heavy weapons can get a devastating first round.

I generally tend to go for heavy weapons (with some weapon speed boosters - these seem to stack up, as most other enhancements can't be bought multiple times and give you a "you already have one" message when you try to buy another). After all, the opponent isn't too quick either. But I have yet to try a run in that Kestrel layout B.
I think the OP is very right. The game is very unbalanced from a "logical" point of view. The shield recharge rate makes diferences between different laser types negligible, unless you have several laser weapons installed, of course.

@catwhowlaks: "I simply don't agree with you" is not an argument.... looks like more pure fanboyism... I've seen you have been playing the game for weeks as you stated in another thread, and for thinking there are NOT weapon upgrades, that is a bit weird since this quote is from the quick starting guide you wrote: "Ship upgrades are also a matter of taste, but also depend on how far along you are and what equipment you have picked up. You should only upgrade weapons if you need the power for additional weapons you have picked up, or want to be able to take damage to your weapon systems without losing your weapons."
Post edited September 16, 2012 by Lobuno
in that quote he means upgrade the ships sysem "weapons" to power more weapons, not upgrade the weapons themselves.

I agree that it doesn't seem like there is a huge advantage to some of the mk2 and mk3 weapons at first glance, but sometimes having the extra oomph is well worth the extra power expense, you just might need to hang onto a late model weapon system till later in the game, and keep using the mk1 versions until you can affortd to spend the scrap on upgading the weapons system of the ship.
Yeah, that quote is talking about upgrading your weapons stat, not necessarily the weapons themselves.

And it's not fanboyism. I have indeed found the different types of weapons to be useful in the right circumstances. That does not mean that balance adjustments might be needed, just that it isn't the clear upgrades are always bad situation the OP thinks it is.

Yes, using boarding instead of weapons is viable and there is even a hidden ship design that has no weapons at all, just a teleporter.
Indeed. Just made a run with the Red Tail (Kestrel type B), and the four cheap light lasers seemed overpowered until end-game, where they proved completely useless.

So I did resort to boarding mostly. And that was great. I did some mistakes in front of the flagship (or, more specifically, there are some moments where I fail to beam my crew back, without understanding why, so they end up killed before I can heal them - it's not a matter of cooldown, maybe a matter of being middle in a fight but this didn't seem to pose any problem at other times). But so far I'm impressed with the efficiency of this method, and I'll focus more on shield+teleport in my next few runs.

The flagship's weapon systems are defended by one gunner each, and are separated from the rest of the ship : take them down, no rebel reinforcement, no repair crew can come to rearm the flagship.

Probably jumps away though. Couldn't test it : made the mistake of sending my team in a wide room, where all the flagship soldiers came to meet them, as, as I said, the (fully operative) teleporter suddenly refused to beam them back for some reason. Next time I'll try to disable all the flagship's weapons (I didn't care for the harmless one), or at least to attack its sensors first.

Anyway, my tiny lasers themselves were not doing much to that well-shielded ship. I don't think the OP's point is very valid near the end of the game.
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Telika: Indeed. Just made a run with the Red Tail (Kestrel type B), and the four cheap light lasers seemed overpowered until end-game, where they proved completely useless.
Yes. I would say Kestrel type B is harder to win with than type A for this reason. With type A you start with a couple of good weapons and you need to find two good ones more; with type B you need to find four since the starting weapons only function well as a battery, and later on that battery is underpowered.

If your ship has 4 weapon slots and your main strategy is just to shoot them all until the enemy is dead then yeah, the very high end weapons are probably not the best option for that. But the situation changes if you have for example three slots, or you are using missile weapons that you don't want to use all the time.
Kestrel B, huh... haven't unlocked yet, achievements sound like a lot of work.
Torus B is also a radical departure from the A, not all for the better. You get heavier guns, but no offensive drones. No sensors, 1 crew member. Power demand through the roof: all repairs and intruder defense have to be done by drones. I'm thinking of venting the hull, leaving everything, but the cockpit, in pure vacuum.
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grviper: Kestrel B, huh... haven't unlocked yet, achievements sound like a lot of work.
They aren't really. One you can complete just by getting drones, cloaking and teleport. If you get reasonably far you should get both the means and the opportunities to buy all if you so choose. Next easiest is coming back from 1 HP - can happen naturally and not too difficult to cause in purpose either. Note that you can flee a battle, no need to let the enemy to beat you to 1 HP and then win. After fleeing you just need a shop for repairs and you can use one that you already know of, no need to find a new one.