I think overcoming the snaked-distribution model would be a good thing, and should be compensated with control over soldier placement, such as having them spawn only in living quarters or something. This way the player has a few more variables to play with when designing the base defense. Just as a preliminary proposal on this, I'd suggest the following for discussion:
Taking into account the 2-level base system, perhaps it could be done so that aliens only penetrate the top level (of course) and certain top-level structures other than the entrance have links between the levels (hangars?). If it's a 3x4 grid up top, the player must then contend with more than one entrance to his lower level, where the living quarters, etc. are.
These entrances to the lower level should be more centrally located, since the top level is a smaller grid and should perhaps be always centrally located above the bottom level. If the player had multiple transitions centrally located, they would then have some different viable strategies for base layout, depending on fighting style, such as:
1. Concentrate living quarters to one side, to allow soldiers to organize and assault en masse as the aliens come down.
2. Spread living quarters around the perimeter to flank the aliens.
3. Place living quarters as close as possible to transition points to bottle the alien up in the top level.
4. Concentrate transition buildings to one side, but leave one transition building on the other side. Concentrate living quarters next to lone transition to quickly battle their way up to the top level and confront aliens before they reach level 2.
Other factors which could effect the base layout decisions would involve the spawning of scientists and engineers -- where they appear, what the effect of letting them die is, etc.
This would, of course, require additions and modifications to the existing base maps, so it would be a long-term proposal.