If tradition dictates you put in a pickup to amplify the acoustic tone rather than add to or subtract from it, then do the opposite - put in a pickup that is going to influence the tone - make a Strat sound like a Les Paul, or a Les Paul sound like a Strat, that sorta thing.
However, with that said, pickup choice depends on what tones you're going for - do you want a Strat that sounds like a Les Paul? Do you want a Les Paul that sounds like a Tele? Do you want a Tele that sounds like a 335?
Now, you're going to have to get into wood tone somewhat to know what it's going to sound like as far as frequencies, and then you'll have to base your pickup choices on what you want those pickups to add to or subtract from that base tone.
Body shape will also have some influence on what the pickups reproduce - a V-shape where most of the wood goes away from the pickups rather than surrounding them (like a Strat/LP/Tele) will generally focus the mids (Schenker, Downing, etc), whereas a more traditional shape will more or less balance the tones (which is why they're traditional and in such wide use).