I used to play the university a lot, but the other factions are well positioned to counter them. Hunter Seeker is THE must get secret project for them. The biggest weakness of the University is their weak military, and their tendency to focus on ideas at the expense of things. It's nice to get chaos guns first, but it does you little good when the enemy is kicking your door down with missile infantry, and you still have to prototype. They're a good builder faction, but then again so are the morganites, and so is the UN.
Some tricks I like to use:
In chess, it's often possible to win by sacrificing your pieces one by one, but making sure you come out ahead at the end. In SMAC, you can create nerve gas needlejets, en masse, and go for broke. Their defenses won't withstand the attack, and their cities will be decimated. The cost? Sanctions forever, and a bad reputation. The benefit? You can cripple eveyone else with extreme prejudice, and follow up with a conquest win.
The easiest military strategy is air power and drop troops. Period.
In my last game, I terraformed almost entirely forests and mines. The upkeep on hybrid forests and tree farms is high, but worth it for large bases. You get solid production, and growth (with tree farms anyway). I put supply crawlers on the mines for extra minerals.
Always have a secret project or two near completion. You might get the tech for a new one, and you can switch over and pick it up quickly.
Jets make good defenders. I tend to have a couple of high production cities crank out clean reactor needlejets. When the enemy attacks, you swoop in with jets and wipe out his units in a preemptive strike.
Use jets to block enemy reinforcements. Most units can't attack them, as they aren't AA.
By the same token, AA rovers are a fun and cheap way to deal with enemy jets.
Virtual world is a great wonder. You're always going to have drone problems on higher difficulties, and hologram theaters have an upkeep of 3. Network nodes have an upkeep of 1. Go figure.
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