只更改图例手柄的alpha值比预期的要困难（item.set_alpha(1)明显会导致一些几乎不可见的颜色出现问题）。但您可以设置手柄颜色，使图例具有统一的外观：

from matplotlib import pyplot as plt

#fake data generation
import numpy as np
n = 10
np.random.seed(1234)
gen = np.random.randint(1, 10, n)
samples = np.random.randint(10, 50, n)
colors = np.random.rand(n, 4)
#reduce the alpha values for demonstration purposes
colors[:, 3] = colors[:, 3]/3

fig, ax = plt.subplots(figsize=(10,8))

ax.scatter(gen, samples, c=colors, s=70, marker="o", label="$\\tilde{y}$", zorder=-100)
ax.scatter(samples, gen, c=colors, s=50, marker="x", label="$\\tilde{x}$", zorder=-100)

l = ax.legend()

for item in l.legendHandles:
    item.set_color("black")

plt.show()

样本输出：