Let's take a look at Tzeentch vs Nurgle matchup. Both factions have a cap of 6 flying units but 6 best Tzeentchean flyers are much better than any 6 flyers of Nurgle.

For instance, 2x Changebringers + 2x Doom knights + 2x Screamers are literally uncontestable, they can faceroll 6x Nurgle Furies, they can beat 6x Rot Flies or 6x Whatever-Nurgle-Has.

In fact 2x $1500 ($1700 ROR) Doom Knights + 2x $700 Screamers are good enough to deal with any 6 aerial units of Nurgle which allows Changebringers to do whatever they want.

Actually the problem of Changebringers is that they are a glass cannon without a "glass" component because they are unreachable for anything that can't fly/shoot and Tzeentch can deploy better aerial units than anything Nurgle (or Khorne) has because the cap only takes units into account, not their cost.

It's even worse when you play 2v2 and face two Tzeentches. There can be up to 8x very strong aerial units + 4x Changebringers that can restore ammo twice thanks to Exalted Pinks. And if you are playing a combo of factions where at least one doesn't have any strong aerial units - that's it, you can't change factions anymore, your teammates "Flying units" caps are wasted and Tzeentches are gonna flame you from above for the whole match. 

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Theo91#7431 wrote:

MP balancing is quite tricky tho whilst still maintaining faction identity and asymmetry. 

I’m not saying it’s correct that you get ‘broken’ match ups but I also wouldn’t want to see factions lose their identity for MP balance.

​It's not that tricky if you obey to one rule "All units must be cost effective but to maintain factions identity we can restrict factions access to certain TIERS of units". The best example is Bretonnia - they have low-tier, mid-tier and God-tier cav options, but they only have low-tier infantry and low-tier ranged. Keep in mind that their low-tier units are very good for what they cost, so their $325 Men at arms and $400 bowmen are very competitive if you compare them to similarly priced units of other factions. Bret just doesn't have high-tier ranged and high-tier infantry which makes them a unique cavalry-focused faction.

Theo91#7431 wrote:

Maybe a solution is to give certain races a ‘handicap’ against certain factions based on community feedback. So maybe give nurgle extra starting gold vs Tzeentch as an example 

I don't think it is possible. What if you are playing 2v2 match Nurgle + Tzeentch vs Tzeentch + VCounts.

Nurgle doesn't have any problems with VC and well... Tzeentch doesn't have problems vs another Tzeentch. So it's not possible to decide who to buff in this situation.

The solution could be to replace unit caps with gold caps for flying units i.e. instead of "You can pick any 6 flying units" -> "You can spend up to 4000 gold on all your flying units".

The problem with Tzeentch is that it can fit 10200 worth of units in their cap of 6 (2x Changebringers + 2x Knights of Doom + 1x Knights of Doom ROR + flying lord).  Nurgle can fit up to 5700 (flying lord + 5x Furies). 

If you are a masochist, then you can replace Furies with Rot Flies but those are not worth their $900 price tag so you are effectively playing with 5x units that perform like $700 but you just wasted an extra 1k gold on them.