Thunder will evolve into Thunder 2, then 3 as you level up.But it removes the risk. Before you had the risk of losing Fire IV completely if you screwed up. That heightened the stakes and made things far more interesting for me personally. Anyway, that's just me. We will see what they come up with I guess. It could make more sense with the other skills they add.
What I am getting at with the Thunder thing is: at level 60 you want a quick casting, low mana Thunder spell to put the dot up and you want the full Thunder 3 for the Thundercloud. How will the game know which one you want at each point? I don't think you would be able to switch traits on the fly in a fight. Maybe they will just modify the Thundercloud effect as you said and give a basic Thunder spell to cast because giving a fast casting, low mana Thunderspell that does the damage of Thunder 3 would be a big buff. Not that I would complain about that...
Thunder's cast time and mana cost are likely to remain the same, but its potency is going to be upgraded as you level up. Casting Thunder will be functionally identical to casting Thunder right now, using your proc will be functionally identical to using your proc right now. You'll have one button instead of 2 (and a dead third button) for the same thing.
Hardcasting Thunder 3 is never a proper decision in the game right now, and Thunder 2 might as well not exist so it makes sense that they're a candidate for consolidation into a single button.