Tips: 1) Early on you shouldn't worry about rarity. 2) Late game rarity is important but not as important as synergy.
It says in game that units of higher rarity evolves better. It seems to me that this is true regarding leveling, but not training. Therefor any unit you do not intend to level can be choosen without taking rarity into account. You should instead consider synergy and secondly stats.
When choosing units for your final team then rarity matters, but getting a rare unit and training it early on might very well result in a unit with higher stats a late game unique, at least it seems that way to me. Regardless of which gets the better stats though, having a team that works well together is absolutely key late game and having a rare that fits well with your team is much better then having a unique that fits decently.