Since this is the first time I've worked on a map that (should) expect real gameplay, I would prefer that we use an established template, and then work kinks out from there.
For this, I turned to ns_tanith:
I extracted the important areas and came up with the following. Red are hives, green are nodes (not terribly important right now, but I left them in for scope clarity) and of course, cyan is Cargo, which I'll refer to as the secondary objective:
I suggest (as the picture indicates) that the control room be placed where cargo would be, moved slightly toward marine start, as the room is useless without the triggers, which are much deeper in the map (likely one in each hive, altered for balance), and also because the room makes for a good ambush point for game flow.
Besides that, I would leave the map with similar flow to Tanith, which makes things simple for someone putting it together, and should make it intuitive to new players.
On a personal note, I think that having one unique element to a map (similar to Cargo) is a very positive thing - it changes the map from "oh look, a new hill to walk on, I'll play on this for sure" into a truly unique experience, and while I know as well as anyone how frustrating and unintuitive an overcomplicated map can be, I think this layout design won't have that effect since it should end up fairly intuitive as it's similar to what people are used to.
What are your thoughts?
