So, why do you think it is bad? What do you think is a better game design?
Units that counter other units felt like a huge improvement in Civ over the att/def system. In Civ 2, there was no way to counter a particular unit except to attack it with something with higher att than its def, or defend with something with higher def than its att, or just to charge it with lots of units. It seemed pretty simplistic, and when you reached the endgame, howitzers beat everything, including other howitzers.
I'd say that the system in Dominions 4 makes a fun game, but at the same time a huge amount of the units (especially summons) are ignored by players because they're either not useful, too weak, too expensive, there are better units which you can afford instead, or w/e. Basically, there are a ton of units, they don't use RPS, they have a lot of combat stats, and they aren't really balanced per se.
The thing about a RPS design is that it makes it far, far easier to balance the units - you're not balancing them against every other unit in the game anymore. E.G. For a simple RTS, imagine you're making three research/building trees for three categories of units, you balance each category of units within their own category so they're better and more expensive or w/e as you proceed in research, and then you can just make sure that each one can beat the equivalent one from the category it's supposed to beat. Obviously that makes it sound relatively dull and simple, but they generally have their own mechanics and so forth to be fun and interesting. It's just that you don't need to test every unit against every other unit anymore and try to make sure they are all evenly matched somehow.
I'm not saying that it's what I would prefer to do, it just seems like it would make things easier from a design and balancing perspective. (And from a player's perspective, you can look at a unit and know what it's good against and what it's vulnerable to)