The class of simple groups isn't elementary. To see this, first note that if it were, then an ultraproduct of simple groups would be simple. But an ultraproduct of the finite alternating groups is clearly not simple. (An $n$-cycle cannot be expressed as a product of less than $n/3$ conjugates of $(1 2 3)$ and so an ultraproduct of $n$-cycyles doesn't lie in the normal closure of the ultraproduct of $(1 2 3)$. )

As for your third question, Shelah has constructed a group $G$ of cardinality $\omega_{1}$ which has no uncountable proper subgroups. Clearly $Z(G)$ is countable. Consider $H = G/Z(G)$. Then $H$ also has no uncountable proper subgroups.Furthermore, every nontrivial conjugacy class of $H$ is uncountable and it follows that $H$ is simple.