We establish several new lower bounds on the $g$-numbers of simplicial spheres without large missing faces. For this class of spheres, we derive bounds on the $g$-numbers in terms of the independence numbers of their graphs, extending a result of Chudnovsky and Nevo. As a consequence, we show that flag $(d-1)$-spheres -- and more generally, flag normal $(d-1)$-pseudomanifolds -- satisfy $g_2\geq (1/2-δ(d))f_0$, where $δ(d)$ is a function of $d$ with $δ(d)\to 0$ as $d\to \infty$. We further prove that, for simplicial $(d-1)$-spheres without large missing faces, an initial segment of the $g$-vector forms a level sequence, yielding additional inequalities among the $g$-numbers. Finally, we show that simplicial $4$-spheres without missing faces of dimension greater than two satisfy $g_2\geq \frac{2}{5}f_0 - \frac{6}{5}$.