I've been thinking: Whose bright idea (in-universe) it was to place engineers, scientist, and soldiers in same underground base? Why not do research and development in laboratories scattered around the world? I mean, they've had internet in 1999, no need to do everything in one place. Why manufacture items and crafts in combat bases, rather than place workshops near industrial centres, where supplying them with raw resources, vast amounts of metal and electrical energy would be less suspicious? Or just use trusted independent contractors? (as bonus, game would not be so hilariously easy money-wise once you discover Laser Cannon)
Offmap research would be harder to do (need to do some mechanism where scientist are paid per project only while they work, and not hired permanently), but to abstract offmap manufacture, all you'd have to be able to do, would be allowing to: make items available to be bought only once certain tech is discovered (and not just "everything from start"), make Elerium part of price (Allen Alloys costs can be included in price), and to specify how long it takes for bought items to arrive separately from between-bases transfer (isn't last thing already in?).
