There isn't a card in this game that is completely without reason to upgrade.
Relic - moot since the unupped is also worthless.
Boneyard - unupped for rainbows, but in a mono-death, the swarm is doubled in attack. That's significant.
Stone Skin - halved cost. Yes, it's negligible, but there are games where a single quantum or health point decides.
Luciferin - allows import to non-light decks for a light splash.
Vulture - decks based around this card often take a while to stack the damage high. That's 1 more damage for every turn you have the Vulture out, which is far from insignificant. Say it lasts for 8 turns and one creature is killed per turn. That's 0+1...7=28 damage unupped, 1+2...8=36 damage upped.
Giant frog is tied with graboid for the most cost effective creature in the game at 5 damage for 2 cost.
Graboid costs 4, but yeah.
Every card is worth upgrading except the Relic, though many are smaller upgrades and should be done last. Here's a non-comprehensive list of cards which are worth keeping copies of both upped and not:
Guardian Angel | Archangel
Druidic Staff | Jade Staff
Firefly | Elite Firefly
Firefly Queen | Elite Queen
Flying Weapon | Animate Weapon (unupped allows you to know which quantum you're spending, potentially useful for rainbows)
Rage Potion | Rage Elixir
Boneyard | Graveyard
Purify | Purify (Allows import, but once again it can be nice to know what you'll spend)
Toadfish | Puffer Fish
Chaos Seed | Chaos Power
Dissipation Shield | Dissipation Field
Fallen Elf | Fallen Druid
Mutation | Improved Mutation
Nova | Supernova
The following creatures begin under 6 health and arrive at 6 health when upped, making them vulnerable to Gravity Shield:
Graviton Fire Eater | Graviton Firemaster
Black Dragon | Obsidian Dragon
Blue Crawler | Abyss Crawler
Purple Dragon | Amethyst Dragon
With an 1 damage blocking shield they are both equally strong with 2 damage blocking shield Giant Frog will do 1 damage more, but without shields Horned will do 1 damage more. So I would say its balanced(if adrenalined). Yeah with 3+ damage blocking shields Horned Frog will not do any damage at all, but even Giant Frog will only do 3 damage and you will probably lose anyway.
But you are right you will not have all frogs adrenalined.
With a one-damage shield, Horned does 2 while Giant does 4. With a two-shield, Horned does 1 while Giant does 3. Diamond Shield will reduce Giant Frog to TWO damage.