Just a short re-cap - there are 2 main concenrnes
1) Without some restrictions, players will always be the same base layout
2) With good base design it is possible to bottleneck the alien advance, making the base defense too easy.
Now, the first point is bogus, since different bases have different buildings, and therefore, can't have an exact layout. No two bases I own are exactly the same. Altough I technicly could make a generic base with 1 of each, but that is just inefficient.
The second "problem" is an interesting one. On one hand, you want the player to be challenged, on the other, you want to reward smart playing. so a smart enough player will have it easy? So? Power gamers have always done so in all games. Be careful not to go overboard.
Now, having all of your team spawn at the CC is no-no. It's just stupid. Have it randomized, so that soldiers spawn either in the barracks/armory/crew quarters or in the CC (a minimum of 2 will ALWAYS spawn in the CC).
Or maybe it should depends also on when is the UFO detected?
Makes sense that if it's detected before it reaches the base, that the soldiers will already be prepared and in positions. So the positioning/spawning on soldiers can depend on that.
Get caught by surprise and your soldiers will be randomly put all over the place. Detect it early, and your soldiers will be ready near the entrances.
So...any building that has above surface structures can be used as a entry point...more or less.
Now, IMHO hangars should be more like missile silos - no doors on them except the big sliding one. But the aliens can blow a entry hole.
The second issue is the number of entrances. Bases usually have 1 or 2, and that is. Which mean that if there are any extra entrances, they shouldn't be "natural" (built by man", but rather alien-made (by blowing holes in walls). With a few randomized holes you can create quite a hectic situation.