[Legbreaker]

Another point is that the Colonial Marines Technical Manual was written well, well after the movie by a fairly talented and motivated fan. It's a damn fine publication, but in no way is it the movie.
For all we know, the Sulaco only held a single platoon worth of marines, one half of which was deleted for the mission to allow carriage of Ripley and Burke, which would explain why there was a spare dropship aboard.
If the ship was big enough to carry thousands of troops, would the marines really have had to carry out all the pre-mission checks and loading themselves, or would there have been specialists available as you might see on an aircraft carrier?
The size of the mess hall we see in the early stages of the movie is also an indication of the limited size and carrying capacity of the Sulaco.

Now, as for the bunching in the atmosphere processor, it's human nature to group together like that in unfamiliar situations. Totally against tactical common sense, true, but those were also some very tight areas. My guess is that if they'd spread out it may have actually worked against them given the aliens could have picked them off one by one at their leisure.

The 3 eggs on the dropship is something I don't buy either. The whole 3rd movie was a disappointment as far as I'm concerned. Sure there were some nice highlights, but the overall concept and storyline just didn't' hang together for me.
I had the opportunity to read the original draft for the 3rd movie a couple of years back - COMPLETELY different. Set on a space station, Ripely was injured early on and in a coma most of the duration, Hicks lives and becomes the hero and I can't remember what happened to Newt (survived I think). Bishop also got a run as well, but again I can't remember details. Ends in an evac of the station by a handful of survivors.
Some of the ideas were a bit dodgy, but as it was only a first draft....