I'll freely admit that I haven't had much of a chance to play around with the modules in question, which is partly what I'm going to be bringing up. However, these are my thoughts on the tech progression:

*It takes way, WAY too long to get any kind of fleet assist module researched. If you take into account the need for high logistics, it's a far better use of your research to go after more advanced weapons, especially considering how cheap those techs have become.
*Once you DO research them, you're done. That's it, there's nothing more to find. Even the race that does have a second, more powerful fleet assist module only has the one.

I'd suggest that the "preproduction" tech that paves the way for fleet modules be removed entirely. Instead, there should be a longer line of techs that give progressively more powerful fleet modules, and/or substantially reducing cost and space requirements. For instance, you could have a "targeting computer" line that gives a 15% bonus with smaller and smaller components, and then follow it with a "fleet coordinator" line that gives a 20% bonus, etc. In this way, upgrading your fleet components becomes a viable weapons path as well, and researching stops being a on-off, very expensive pair of techs.

A secondary concern with the modules:
*Fleet attack modules don't stack with fleet defense modules, which severely limits the utility of mothership or carrier type craft, and really makes researching BOTH types of modules completely pointless.
*Giving targeting computers to multiple ships in a fleet does nothing but waste space. I can understand the balancing concerns here, as well as the "the first computer does all the work there is to be done" argument, but couldn't successive modules simply have a smaller and smaller effect on the fleet?

One option is to make fleet modules smaller, and give them less effect. IE, a tulon weapons focus only gives a 5% bonus. To compensate, however, a ship may mount multiple fleet components.