Hmm, then I have been a bit unclear. In general factories are not meant to be unbalanced or counter each other. To help explain this, I'll say a set of factories, X, is 'balanced' if:
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The matchup between any pair of factories in X has a 50% winrate.
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The matchup between all pairs of factories inX and notInX is never in the favour of notInX.
In practice no game is going to look like this, but it is a useful ideal to have in mind. A map has three balanced factories if, when playing on that map, there is a balanced set of factories that includes at least three factories.
I'll state my minimal aims for factory choice in 1v1:
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Land maps should each have at least three balanced non-air factories.
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Every non-air factory land should be a balanced factory on many common land maps (say, at least 40% of maps).
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Both air factories should be viable secondary factories in many situations.
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Making a land factory as your second factory should be good in some situations.
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Sea maps should have a set of balanced factories that include ships.
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Each of the other four sea factories should be viable as secondary sea factories in many situations.
Keep in mind that these are my minimal aims. More is generally better. I would prefer for there to be at least four or five balanced factories on land maps, and this is perhaps my strongest deviation from these aims. Being able to start non-ships in a sea 1v1 is fine, but not required. More viable options for second or third factories is preferable.
The 1v1 goals are fairly easy to extend to larger games. If there are many viable start and secondary factories then there are many options for players to pick.
How does this all relate to unit balance? It doesn't really. Factory balance is the real important factor for competitive balance. Some factories may have holes or great units, and it is generally fine given my factory balance goals are satisfied. This is all diversity that doesn't have to conflict with competitive play. That said, I have some aims for units that are similar to what I wrote for factories:
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Every unit should have a situation where it is the best unit for the job, across all factories.
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At least four units from each factory should be fairly common in all matchups.
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Non-specialist units (not AA, bombs, weird scouts, utility etc..) should have a matchup where they commonly occur.