The adjacency bonus system is a really unique and cool feature in Supcom, but after the early T1 massfab farming episode in Vanilla Supcom, I feel that its potential was really cut back and never given much thought from that point on.
While Supcom isn't susposed to be Sim City, base building and economic efficiency are a part of the game that really sets Supcom appart from the RTS field and is enjoyed by large proportion of the playerbase. The game is (as it should be) balanced toward dynamic offence and territorial (mass point) control, but I feel that there could still be a more fully realised and rewarding adjacency system implemented without upsetting that focus. The designers built in the excellent chain-volatility feature for risk reward and all adjacencys are just numbers that can be infinitely tweaked.
As things stand, you only really see two adjacencies used in most games, Mass storage around Mexes and Power Gens plugged into Factories. Mass storage around Mexes is good, because it puts even more importance on what is (and should be) the main confict reource in the game, the mass points, but it is so rewarding that no other type of mass adjacency is ever worth using. It would be interesting, for instance, if say, plugging your Mexes into factories was truly worthwhile for 'certain' early build orders in the same way that plugging power into air factories is for going air-tech builds. Like on a 5x5 landspam map where early mass consumption efficiency was emphasised over maxing out late game income.
There are many more examples that Im sure people can come up with. There was a huge amount of cranial energy devoted to this topic early in Vanilla on the GPG boards by many players who enjoyed the economy as much as any area of the game, and Star Craft 2's popularity shows how much players enjoy a deep build options game. Since, as I already noted, that adjacencies are just number that can be tweaked and there is the inbuilt chain-volatility feature, it would be a low risk and high reward investment of time to look into realising F.A's fantastic adjacency system's unrealised potential.