In 1973, Lemmens and Seidel posed the problem of determining the maximum number of equiangular lines in $\mathbb{R}^r$ with angle $\arccos(\alpha)$ and gave a partial answer in the regime $r \leq 1/\alpha^2 - 2$. At the other extreme where $r$ is at least exponential in $1/\alpha$, recent breakthroughs have led to an almost complete resolution of this problem. In this paper, we introduce a new method for obtaining upper bounds which unifies and improves upon previous approaches, thereby bridging the gap between the aforementioned regimes, as well as significantly extending or improving all previously known bounds when $r \geq 1/\alpha^2 - 2$. Our method is based on orthogonal projection of matrices with respect to the Frobenius inner product and it also yields the first extension of the Alon-Boppana theorem to dense graphs, with equality for strongly regular graphs corresponding to $\binom{r+1}{2}$ equiangular lines in $\mathbb{R}^r$. Applications of our method in the complex setting will be discussed as well.

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