Re: Small ships vs Big ships
PVK hit on my favorite mid-to-late-game usage of small ships; nuisance ships.
While your main battle fleets engage the larger enemy ships, send small recon fleets of smaller ships. Even if they just sit in an enemy system, they lower happiness and (hopefully) start a few riots, destroy a few unguarded transports or colonizers, etc; just annoy the heck out of the inner systems and keep 'em chasing YOU. See how quickly many will retreat to restore peace and order (and income!!!) to their monetary infrastructure.
Just my $.02
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