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That might actually be a more preferable scenario, since you would have troops on the ground ASAP, rather than having to send your troop transport. Basically, you'd have no friendly casualties or cargo losses at mission start, which you would/should have if you're scrambling to assist.

It also might be a fun thing to assign rookies or some such to defend shipments, leading to a small fight if ambushed or something

I like any idea that makes the geoscape more interesting. Currently, the only spatial element of the geoscape is radar coverage and interceptor range. In terms of something that can make X2 stand out, from X1 and from XCOM, the geoscape has a lot of potential. At the moment the geoscape is a very un-stimulating environment. For a game that falls into the strategy genre, this feels like a bit of a waste.

The way I'd implement it is that each base has it's own storage, but as long as supply lines are in tact, every base has access to materials from other bases - although there is a small fixed penalty when working on things were resources aren't local (like +5 hours to production time, to simulate shipping time). Supply lines would work sorta like the internet routing - as long as one base can trace a connection to another, it can get resources from it. Players would place supply lines between bases manually and each supply line would have to be maintained. There would be a cost associated with it, and the distance would also factor into the cost (so a 4000km long supply line might cost 4000$ monthly to maintain). What this means that you CAN connect every base to every other base, but it would cost you a lot, so it might not be the most optimal solution. The beauty of this system is that it's simple and intuitive without being clunky and requireing tons of micro-managment. With the added bonus of it tying into the goescape and battlescape, due to supply lines being interractable. In terms of generated missions, alien could attack in 2 ways: air strike or ground ambush. Ground ambush would generate open maps with roads or train tracks, where a train or military convoy would be on the defensive. AI controlled soliders, in the form of train/convoy defense, would be on the map. Possibly a crashed cargo plane map? Air strike would be geoscape only, with your interceptors scrambled to defend, with convoy escorts and local defenses buying time.