Honestly, the best route to take with what are essentially going to be one-shot EW platforms is (like many things) lifted from Weber: Don't bother with stealth, just build them as small as possible and seeds dozens of them wherever you think the enemy will be. On a related note, it tends to be easier to spam FACs than slow/stationary platforms that need to be transported, especially if you've dumped a lot of RP into mesons. I typically end up with large strike groups composed of scores of FACs in every major system by the time I've reached TL5 (at least, I did in pre-6.00 games; they're going to be decidedly harder to support now), with the bonus that in addition to swarming enemies they can also be used as cheap, throwaway garrison units, which in turn allows you to use your real warships for important things.
That said, the changes to fuel usage and crew morale have caused something of a paradigm shift for FACs; now they pretty much have to be used either as in-system defence forces or with carrier support.
What I really wish we had is bomb-pumped X-ray laser satellites (i.e. stationary laser warheads), akin to those used in the Starfire novelizations. Or, indeed, the ability to produce any sort of crewless non-missile weapon. Actually, that has always been one of the things which bugged me the most: crew for small vessels is completely out of proportion; "fighters" are more like PT boats, while FACs can have easily ten times the crew of a Space Shuttle mission.