A Jarrasul Evacuator does 1,500 damage or more with its Drain Planet ability. This also gives you credits and does the damage faster than Raze Planet. While it takes a long time to recharge, it still has far more bonuses than Raze Planet. It's not just a little better, it's a lot better. Keep in mind that the mentioned ability is for a colony capital. (1)
Not only does the Kol have weapons pointing in pretty much every direction, making it much harder, target priority comes into the equation twice. For instance, you have your Kol fighting a militia Kodiak and its usual supporting Javelis/Krosovs/etc., you have to choose: Am I going to get their biggest gun out faster or not? Am I going to waste 75 antimatter on something doing not nearly as much damage or not?
Even when you've got four Kodiaks facing down a Kol, it's still better to keep focused on one target. It's always better to get that gun off your ship faster and not give the enemy a chance to recover. (2)
The value of your fleet and its capabilities shouldn't be a percentage, it should be a number.
Let's say Kodiaks are worth 20 "value points", Kols worth 60-100, and so on. Most things don't lose value when the enemy's economy inflates to ridiculousness. (3)
On that matter, let's look at Cobalts; do they lose their value as the game progresses on? No, they might even be more worth their cost thanks to their unlockable abilities.
Do scouts lose their potential as the game continues? No, remote sensors and timed explosives are marvelous, especially if you need to monitor an uncolonizable without keeping a unit there. (4)
(1) Yes, and even better than that is the TEC superweapon. But how long will it take you to get there? I should have qualified this a little better, yes, but saying a lvl 6 ability is better than an ability that you can choose right off the bat (although normally, you'd probably get it second if you were going for it) is not necessarily true. Smaller games might not even let a single capital ship level to 6, for example.
Then there are the other factors to take into account. These abilities don't exist in a pile in a warehouse that you pick and choose from, they come as part of a total package. The total package of the Marza in most multiplayer games (this is what we're talking about, I assume) is much better than the total package of the Space Whale (also they're obviously two separate races, a pre-game mitigating factor).
To compare them more easily, imagine that the Space Whale had the Marza's ability as an extra option while losing the lvl 6 option of Drain Planet. In the slightly-larger-than-very-small games where Marzas and Space Whales would come into play, the Space Whale would arguably be BETTER off this way than it is now. Hopefully, that makes what I meant a little clearer. My apologies for the incomplete statement.
(2) Honestly, in these situations, it doesn't even matter. If you're talking about killing militia to take a planet, that's a very insignificant fight or at least not a fight where something like Gauss Cannon will matter very much (aside from speeding things up). In your specific example, why not open fire with Gauss, then finish the job? If you don't have enough energy, the question of who to fire upon is pointless.
The real question behind all this is: does the ability do a good amount of damage? In most fights with another player, the damage inflicted by this ability is significant, even with 'wasted' damage from mitigation. If the listed damage was lowered and changed to ignore mitigation, would there still be a problem - that is, is it all just psychological? Having a discussion about the particular examples you cite won't really lead us to an answer of that question.
A slightly more pointed question would be about whether or not the Kol is balanced with other battleships early/mid/late game. The fact that one chooses Gauss as the first Kol ability already says that it's the 'optimal' choice - the question of the topic is 'is it optimal enough?'. I feel it probably is, but I can't demonstrate it to you objectively (nor you can do the same for the opposite argument) because it's a rather subtle issue that probably only gives an answer with lots of playtesting.
(3) That's not correct. If you assign a number of value points and add them all up, you will get a total. Let's say you have 5 ships worth 1 point each. You have a total of 5 points. Each ship is worth 20% of the total value that you have. Now you build another ship, and have 6 - total 6 points. Each ship is now worth 16.6% of your total.
The absolute value of each ship is the same (it will never change in this simplified example). However, the relative value will always decrease as you get more total points. So, by analogy, the longer a game goes on and the more total points you gain (including points for planets, economy, logistics, whatever), the smaller relative value each individual bit has.
Now you CAN increase the absolute value (and therefore, relative value) of ships and capitals by researching (and leveling). Abilities can have their relative (and absolute) values increased as well. But those are discrete one-time events. As a whole, everything will decrease in relative value as you gain more 'stuff.'
The ability (given that it's level 3 to simplify the example) will always have the same absolute value. But if you build another ship (or trade port or whatever), it will be worth less to you than it was before.
Now, I think what you're trying to say is that the value 'curve' for this ability is too 'flat' near the latter part of the game (when compared with the later-game economy). Others also think that it's too 'steep' at the beginning of the game. In other words, at the beginning, the relative value of the ability is extremely high, and at the end, it's extremely low (in longer games).
Some might say that balances the ability, but I would disagree because that's an ugly 'curve' to have for anything, and it's totally inelegant. They'd probably benefit from reducing the effectiveness of the first level and increasing the effectiveness of the third level or rescaling the whole thing as a percentage or something.
If I still have misunderstood you, please correct me.
(4) In both of these examples, the ships have experienced an increase in their absolute value, and therefore also in their relative value. Abilities experience EXACTLY the same kind of increase when levelled so this particular argument doesn't work.