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It would be interesting to discuss the pros and cons of the two upgrade options for monsters, as well as the situations where one upgrade is preferable over the other. To start the discussion, I will share my opinions (which are quite superficial, as I have only been playing Heroes 5 recently).
Hunters are a one-time use weapon (they are eliminated shortly after being discovered), so Assassins are stronger.
Megeras seem to have better stats (defense and survivability) than Furies. Megeras usually have enough initiative.
The advantage of Overseer Minotaurs in almost all parameters seems to outweigh the double strike of Guardian Minotaurs. Guardians are preferable if they are the main attacking force of the army.
Dark Riders seem to be better than Swift Riders. The advantage is in damage and initiative, and the charge attack is better than a flanking attack.
Cave Hydras are stronger than Dark Hydras. Better defense, damage, and, most importantly, regeneration are more important than slightly better initiative and acid blood.
Shadow Lords are more useful than Night Hags: a strong ranged attacker is always helpful, and invisibility, judging by the relevant topic, is not a particularly significant advantage.
Red Dragons are stronger than Black Dragons in most cases due to their burning ability, regeneration, and other factors. Black Dragons are better with a weak commander, especially when defending a city.