There appears to be a fundamental difference between Rune Factory Frontier and Rune Factory 2 in the way Monster levels operate. In Rune Factory 2, a Hunter Wolf definitely was superior to a Silver Wolf. Even at 10 Hearts, with as much combat experience as I could give the Silver Wolf, when I was able to tame a Hunter Wolf in the 2nd Generation, he represented a superior Ally even at low heart level.
In Rune Factory Frontier, on the other hand, heart level and the amount of time that a Monster has spent with you in combat situations does create an Ally that is stronger than his 'superior' cousins.
For example, my Silver Wolf at only 7 Hearts had the following:
Level 82, MAX HP 1284, ATK 258, DEF 314, MAG 239
The Hunter Wolf initially is at Level 74 with: MAX HP 1080, ATK 254, DEF 273, MAG 22 which makes the Silver Wolf, with his experience and affection for me, a superior choice.
Heart Levels increase more slowly in Rune Factory Frontier than in Rune Factory 2. In Rune Factory 2, Monsters who never left the Monster Barn increased in heart levels fairly quickly as long as you cared for them properly and made certain they had food. In Rune Factory Frontier, a Monster who never leaves the Monster Barn to accompany you on your peregrinations will increase in Friendship far more slowly than one who does. The entire business of Monster levels and Friendship is a bit more complex in Rune Factory Frontier than in previous Rune Factory games, as Monsters of different types increase in Friendship at different speeds. Some Monsters, put simply, are more disposed to Friendship with humans than others.
In a way, it is rather satisfying to discover that time and energy lavished on a Monster have an intrinsic value and that taming a more powerful Monster may not signify any 'upgrade' when compared with one who has been a loyal and faithful companion throughout your combat experiences.
Note that there are exceptions and this is only an example of two Monsters from the same family. If I were to tame a Mini Dragon and compare it to my trusty Silver Wolf, the Wolf would suffer from the comparison.