So パック called him 好ましい earlier. So that’s the 評価 that he’s referring to. Something like “If I were to choose, I’d have preferred Emilia-tan be the one to say that.”
Then he goes on about the commander and the horse.
I thought this looked like an idiomatic expression so I looked it up in full in my dictionary app. That’s what I usually do with phrases with weird grammar like this, there’s a good chance it’s an expression.
Another translation I found on dictionary.goo.ne.jp is “If you wish to win someone’s heart, you should win over those around him first.／If you wish to achieve a great aim, you should begin by removing all the obstacles.”
So something like if you want to shoot the commander you start with his horse. Only in this case it’s a cat. Would it have the same effect? Subaru wonders.
Edit: Regarding the 方, it’s エミリアたんの方 as opposed to パックの方. You use の方 like this to refer to, for example, just one person out of a party of people.
Regarding 評価 it’s not price/value, it’s more like “how one evaluates something / someone”
In this case it’s referring to what エミリア and パック think about スバル.