I agree with this specific problem a lot - a lot of what makes a good splash doesn't always translate into a good face icon. This causes a problem because you might have to make compromises to one or the other (in this case, Lux's face portrait in-game looks strange because of the sizing).
I'm not an artist (and by that I mean I'm so terrible at art I'm like a nega-artist), but I'm going to kick up some dust about how we might be able to make these different. I think there's two goals for these two pieces of art:
* Splashes should be intricate, high-detail renders of characters so you can get a cool idea of who they are and what they do. It's basically shippable concept art! It's job is to look super sweet.
* Icons present information to players in game. Its job, first and foremost, is to communicate information to players. Additionally, it should "look right" in some way that likely draws little attention to itself outside of the information factor.
Not only do I think separating the assets would solve the problem you lay out here, but I think it also can help make our icons look more clean and readable. And then the artists can focus on making stuff look great, and not hold back when these problems leer about.
Kog'Maw's puking-appendage has been scrubbed from his icon; Kha'Zix is missing the left-half of his body (really noticeably different, actually); Alistar's body has been scrubbed; I think Jax's "hair" has been considerably lightened; Twisted Fate's background has been scrubbed for a flat color; Renekton's background has been recolored to brown from yellow, etc. I'm fairly certain Rengar's has been rotated.