A complete answer to your question is provided by a (difficult) result of Cobham [2].
Given a numeration base $b$, a set of natural numbers is said to be $b$-recognizable if the representations in base $b$ of its elements form a regular language on the alphabet $\{0, 1, \dotsm, b-1\}$. Thus, as you observed, the set of powers of $2$ is $2$-recognizable since it is represented by the regular set $10^*$ on the alphabet $\{0,1\}$. Similarly, the set of powers of $4$ is $2$-recognizable -- it corresponds to the regular set $1(00)^*$ -- and the set of powers of $3$ is $3$-recognizable -- it corresponds to the regular set $10^*$ over the alphabet $\{0,1,2\}$.
A set of natural numbers is said to be ultimately periodic if it is a finite union of arithmetic progressions.
Two bases $b, c > 1$ are said to be multiplicatively dependent if there is an $r > 1$ such that both $b$ and $c$ are powers of $r$: for instance $8$ and $32$ are multiplicatively dependent since $8 = 2^3$ and $8 = 2^5$.
Theorem [Cobham] Let $b$ and $c$ two multiplicatively independent bases. If a set is $b$-recognizable and $c$-recognizable, then it is ultimately periodic.
In particular let $S$ be the set of powers of $3$. We have seen that it is $3$-recognizable. If it was also $2$-recognizable, it would be ultimately periodic, which is certainly not the case for $S$.
Cobham's theorem led to many surprising generalisations and developments. I recommend the survey [1] if you are interested.
[1] V. Bruyère, G. Hansel, C. Michaux, R. Villemaire, Logic and $p$-recognizable sets of integers, Journées Montoises (Mons, 1992). Bull. Belg. Math. Soc. Simon Stevin 1 (1994), no. 2, 191--238. Correction in no. 4, 577.
[2] A. Cobham, Uniform tag sequences, Math. Systems Theory 6 (1972), 164--192.