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Here's my take on unit upgrades:
1) I almost always go for Militia; stunning is a great ability.
2) I almost always choose Archers. They're a convenient unit with no range penalty. I usually don't rely on them in the endgame, but sometimes I upgrade them to Veteran Archers (their melee damage is incredible).
3) This is always a tough choice for me. Both units have useful abilities. I choose based on my strategy (but since I usually train Monks, I take a few Pikemen, and the rest become Monks, who are hard to kill).
4) Griffins usually take a while to build, so they're weaker than other units in the endgame (I don't really like them). I upgrade them to Royal Griffins so they can deal more damage before they die (Archers are good against them).
5) If I train Adepts, removing spells is very useful (they have no competition on the battlefield). Otherwise, I usually choose Imps (especially if I haven't learned Light magic).
6) Since I play Hot Seat with friends, I usually choose Isabella. I only take Paladins if I see that Dark magic will be used.
7) If there will be a lot of melee units in the endgame, I'll take Seraphs; otherwise, I usually take Archangels (resurrection, stability).
That's how I do it. I'm open to suggestions