gem upgrade just some bonus to your progression so is just fine.
but amethyst need to have some new use, only buying new theme just boring
Giving amethyst any use other than buying cosmetics will make it so nobody wants to use them on cosmetics, which would be bad. The whole point of having five different gem currencies that are all gained at the same rate and used for different things is so that you don’t feel bad about spending them.
Are people buying the themes in the first place?
I didn't know where they were, and once I found them the cheapest cost 1000, which would take 40 days to afford. Even at my current rate with 112 achievements it would take 20 days. If you've played long enough to afford a theme I would guess that you've stopped caring about what it looks like, if you even did in the first place.
It wouldn't be choosing between buying a theme and buying an upgrade, it's between buying anything or having a currency accumulating uselessly.
And having to choose what to spend currency on is the main mechanic of idle and incremental games, and it wouldn't be so important if the upgrades didn't take so long to afford in the first place.