Right now, the effects of the composite numbers are extremely logical, but as a result, that means that a lot of gems are just bad (like 81).
I think that if the gem progression were made less rigid, then almost every gem could be made at least interesting. I think this would lead to more varied strategies, as well as add to the thrill of discovering exactly what every gem combination does.
Some ideas that I brainstormed earlier today, not saying this has to be the exact implementations, but just as an example of how less strict progression could go.
The theme of 2 is burning.
2. Fire a range-1 beam in 4 directions, blocked by stones and burning all things it passed over.
4. Fire a range-2 beam in 4 directions, blocked by stones and burning all things it passed over.
8. Fire a range-3 beam in 4 directions, blocked by stones and burning all things it passed over.
16. Fire a range-4 beam in 4 directions, blocked by stones and burning all things it passed over.
32. Fire a range-5 beam in 4 directions, blocked by stones and burning all things it passed over.
64. Fire a range-infinite beam in 4 directions, blocked by stones and burning all things it passed over.
The theme of 3 is card access. Since cards don't really combine very well with other effects, 3 also has a theme of amplification when combined with other effects.
3. Draw 1 card. Discard 1 card.
9. Draw 2 cards. Discard 2 cards.
27. Draw 1 Card.
81. Draw 3 Cards.
Here's a potential 11, and how it would combine with 2 and 3.
11. Diagonal is adjacent, but not orthogonal.
22. Diagonal is adjacent, but not orthogonal. Fire a range-2 beam in 4 diagonal directions, burning squares it passes over.
33. Diagonal is adjacent, in addition to orthogonal. Draw a card. Discard a card.
44. Diagonal is adjacent, but not orthogonal. Fire a range-4 beam in 4 diagonal directions, burning squares it passes over.
66. Diagonal is adjacent, in addition to orthogonal. Fire a range-3 beam in all 8 directions, burning squares it passes over. Draw a card. Discard a card.
88. Diagonal is adjacent, but not orthogonal. Fire a range-infinite beam in 4 diagonal directions, burning squares it passes over.
99. Place this stone anywhere on the board. Draw 2 cards. Discard 2 cards.
Bolded are the additional effects that wouldn't just be implied by the factoring. I think it would make these gems more interesting options.