Re: Are we absolutely sure....
Specialized facilities ALREADY outproduce Monoliths (at the same tech level, of course). For instance, a Mineral Miner generates 800, 900 or 1000 minerals vs. 500, 700, or 900 minerals from a Monolith. Or did you want the resource-specific facilities to generate triple the amount of a Monolith, to make up for the fact that a Monolith generates some of each resource? Although you should also bear in mind the relative costs to build those facilities in the first place (resource-specific facilities are much cheaper than Monoliths).
The only reason I can see for Scanners (or whatever) vs. Robotoid Factories is the build cost. If you have a planet (or system, for the system-wide facilities) that only produces a particular resource, it's cheaper to build the appropriate bonus facility instead of the Robotoid Factory. HOWEVER, the research costs for the resource-specific bonus facilities may not be worth the cost savings. Especially since you also get research and intelligence bonus facilities while researching the Robotoid Factories.
In all, I think some of the facilities were balanced in terms of a high-tech start, but not in terms of a low-tech start. As for the weapons, there've been weapon balance problems since SE3 and SE2. Carriers in SE2 were practically unbeatable; Ripper Beams in both SE2 and SE3 were fairly useless, but Wave Motion Guns were great; Graviton Hellbores in SE3 cost too much to research for the damage ratio. And now in SE4, fighters seem a bit more balanced (though not perfect, it seems); WMG's may now cost too much to research (especially since you have to get Propulsion 8 or 10 or something just to research High-Energy Weapons, and then do all the research to get WMG's). Graviton Hellbores are easier to research than in SE3; the damage ratio still isn't great, but it's practically the only direct-fire weapon with Range 8 (except for WMG's, Anti-Proton Beam 12's, and some of the Organic weapons).
Ah well, enough off-thread ranting...
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