I'm not even going to bother arguing why rock paper scissors is the absolute weakest form of gameplay available to an RTS. Its not worth my time; if you honestly think that it is better than a holistically balanced game like TA, then I think you might be playing the wrong game.
Oh, and let me point out that OTA backfired on this point. In most cases, level 2 where to weak and was never built, with the excetion of gunships. I've read atleast 2 guides that say that you should't tech up. Rather, you should push on with level 1 units untill the enemy dies.
I don't think you have ever really played OTA. I play OTA (as in, not the OTA mod for Spring, but the actual game) fairly regularly; and I haven't seen a gunship for a long time. Which is not to say that they are useless, only that their particular role hasn't been needed in any games thus far.
Level 2 is certainly not weak. The reason they are only rarely built is a sound one. You are not expected to fill out your army with majority level 2 units. That would be inefficient. You build the level 2 units that you need to fill the roles. I don't need thirty goliaths or bulldogs; I need three or four to soak up the damage on the front lines long enough for my light units to do the damage.
I don't need 30 morties. The morties would just get killed by the faster, lighter level one units. However, a few morties at the back of my main level 1 force will
augment my force by providing a long range artillery attack.
Think of a modern army. The main force are your infantry, while you have a few more expensive tanks which serve to support your infantry. Sure, the tanks have got heavy armour and massive firepower - but they are bloody expensive, and have weaknesses of their own. Infact, there are many things that infantry simply do much better than tanks. Which is not to say that tanks have no role, only that you don't need the majority of your army to be tanks, you need the majority of your army to be infantry - which are supported by tanks.
The same goes for OTA. Level one troops are your "infantry". They form the bulk of your forces, and they provide the meat of your warmachine. You should rely on them to do all of your grunt work - they are good in numbers, and often offer excellent speed and firepower for their respective costs.
Once the game progresses, however, you will find that you will need specialty units to fill roles which your grunt forces just can't manage. They may have a powerful line of defenses which your troops just can't crack (heavy tanks, long ranged artillery), or you may want to launch a sneak attack (radar jammer), or you might want to add a bit of power to your armies (mavs, penetrators, etc).
These units do not obsolete the earlier units. Indeed, they can always be bested by earlier units when left unprotected; they have special roles, which they can fulfil excellently when used properly - but they aren't simply "a bigger, better and meaner" version of an earlier tank. You have to use them intelligently throughout your armies, mixing and matching your forces to get the most out of what you need them to do. There should never be a be all and end all super unit, or a combination of units, that always trumps.
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For the people balancing the Krogoth, perhaps a counter unit is not always the best solution. Indeed, counters are often the worst way to fix a problem, as they often result in more problems, such as counter-counters, and counter-counter-counters, etc. The worst situation is when it becomes a matter of "You have a choice of option A and option B. Your player has a choice of option C and option D. Option A beats C, and Option B beats D. You don't have any knowledge about what your enemy is going to do, but you have to take a punt and hope that the option you pick will win."
Of course, that is the fundamental weakness of the Rock-Paper-Scissors balancing strategem; that there is no intelligence at all involved in it.
In terms of balancing the Krogoth, rather than placing some unit that trumps it, you need to look at the Krogoth, and look at its strengths and weaknesses. You have to isolate and define these, and then make them particularly obvious. If the Krogoth is slow as hell, your artillery units can bombard it before it gets in range. If it has a shocking turret rate, your units can run circles around it. If it has poor reload, you can mix your troops with weak cannon fodder and expensive punch-packers to try and draw the krogoth's fire. And then there is the simplest of all, which is what OTA used to balance it. If the Krogoth is massively expensive, and takes ages to build, then it serves the player who falls victim to it right. For the cost of a Krogoth, a player should be able to build an army that can be fielded well before the Krogoth. A player with adequate intelligence can just starve his opponent before the Krogoth is fielded.
As you can see, there are many, many ways to balance things; adding a simple "counter" unit is the easy way out, and almost inevitably backfires.
