I've just started playing TOA after a long hiatus from Gal Civ II. In general I love the new changes, and fleet modules is one of them.
I know that the computer targets ships based on the Attack/(HP+Defense) formula normally, and that fleet modules actually provide a big bonus in this category, making them much more likely to be targetted.
I think this is a good thing for the most part, and it allows me to add some armor to a fleet moduled ship and still have it be targetted, making armor a bit more useful.
However, I think the bonus is too big currently. I can easily take a huge ship, apply a fleet module, and then ramp up its armor to 60 or more while putting a little 3 attack weapon on it. If I put it in a fleet with smaller, completely unarmored high attack ships, the fleet moduled ships are still targetted. The effect of this is I have a near invincible fleet that can take out stronger weaponed and more costly fleets.
For me, its gotten to the point where combat follows the same routine each time. Get big defense, one super ship, apply other ships as need....and win.
Again, I think the idea is a solid one, its simply that the bonus needs to be toned down. I think its great that I can put extra armor on my fleet ship so it takes the pain first, it just shouldn't be such a large ratio. If I had a 30/30 ship taken the beating, makes lots of sense. But when its 3/60 it gets a bit out of hand.