Sun Tzu Wu,
We would always have something "interesting" to build in a city with a factory -- wealth! If we have no other needs for buildings, units, etc., a factory city can always crank out some cash to boost our tech rate.
It is true that factories take time to build, but so do most expensive buildings. Factories do have the advantage of speeding up all following builds. So if we know we are going to build a factory in a given city at some point, there is solid benefit from building it first in order to get maximum benefit.
Other builds may take precedence due to need for beakers, GPP, cash, whatever. This is where player judgement has to decide what is most urgent, and thus this discussion.
But getting those additional hammers going earlier tends to pay off.
You have a good point about needing more base hammers (Mining Inc, levees, whatever) in some cities before a factory will really pay off. At first, only our strongest hammer cities will benefit from a factory. But because they are the strongest cities, we get a large fraction of the total eventual benefit early. These factory boosted cities can then produce wealth or units or wonders (or Mining Inc executives!) while other cities slowly get their factories online.
We do need to think about power for our factories, and about health. Powered factories produce serious health issues (much more than the original "vanilla" Civ IV factories did), and of course we need a power source: coal, nukes, hydro, or Three Gorges (for cities on the main continent).
We already know that we do not have a close, convenient uranium source. Coal will not be revealed until Steam Power, which has the additional advantage of unlocking levees. If we turn out not to have any coal, then factories are going to be much less beneficial.
We would almost have to go for Three Gorges at that point, to at least power our mainland cities.
Maybe grabbing that uranium for insurance is more important than I thought?
I do like your plan to go directly for Biology and hope the AIs will research Corporation for us. The additional trade routes would almost certainly all be internal right now, with many AIs running Merc. By the time Corporation became available by trade, hopefully Economics would have tempted at least some AIs to convert to Free Market and open up foreign trade routes again. We can get boosted farms sooner, and maybe start pushing to Medicine. These are on our path to Research Institutes which we very much want anyway.
Do we have any interest in pushing for the Electricity-Radio-Mass Media wonders? We can probably get the happiness "hit" resources in trade, but Cristo and (to a smaller extent) Eiffel would be nice to have. Both are quite expensive, though, even with iron for Eiffel.