Yeah. I think that's an open, and interesting, question. Facelessclock summed it up well in the OP... Defenses are effective but expensive, and it looks like they're not worth getting for a big part of the game.
It can be frustrating to try to talk it through on forums because so often people end up talking about different things. Shields will feel a certain way to a player who enjoys leisurely game, takes the time to develop his or her empire, and goes to war wth a solid tech and production advantage. In contrast, a player in a masochistic game who strains to win as fast as possible may experience shields differently. This makes it real easy two otherwise reasonable, intelligent people to go back and forth on something like this and never actually talk about the same thing.
So, for the rest of this comment, let me clarify that I'm talking about balance, I mean balance from the perspective of a power gamer trying to win as fast as possible and optimize every choice. Such a player will only research shields if doing so has a higher return, in the form of combat effectiveness per cost, than investing that research in elsewhere.
That said, the way it is right now, from what I can tell, shields aren't worth researching in the beginning of the game. Putting the research points into weapons is a better investment. Later on in the game, when ship attack values get up around 20 or so, the picture becomes less clear. Also, shields are most effective on relatively large, high tech ships fighting relatively smaller, lower-tech ships, which is a scenario that doesn't happen until the mid-game at the earliest.
So, should the damage, size, and cost values be tweaked? Well, we would hope to gain an improvement in gameplay. More of the tech tree would be useful, the experience of deciding how to deck out your ships would be richer and more nuanced. From a subjective point of view, we would hope that the change would result in a net increase in fun (that's a, uh, technical term) for all players; from an obective point of view, power gamers going for "accurate" play would face fewer options where one choice is always inferior, and so could explore more of the "game space" without deviating from accurate play. So that's the benefit, or at least the hoped-for benefit, of tweaking the values. In the real world, we have to admit some uncertainty because the new system could be worse.
What's the cost? Well, there's a small but not insigficant up-front cost (determining and entering better values), and this cost comes from out fixed pool of manhours at Stardock. There's also a big potential downside; I think everyone involved with setting the values where they are now would emphasize that a fair amount of thought and testing went into the process. New values could mess up the balance more. Furthermore, all of the existing third-party tech charts and the information on the wiki would be outdated.
So is it worth a change? Well, I think so, but not in the immediate future. Add modding support and the simultaneous firing system in 1.2, and let those sink in. Get the Library acceptance times down to days instead of months. If there's good feedback between modders trying new things and Stardock incorporating the best new ideas back into the game, then the cost of the change is much smaller. Stardock can take something that works instead of developing it themselves, and there is less uncertainty that it will break the balance because it can be thoroughly tested in a mod first.
I don't know, we'll see what happens. There's room for improvement, I think, but doing the improvement right is tricky. At the same time, it's not really breaking the game outright, and shields are useful in some contexts. I just hope GalCiv2 reaches the level of polish where issues like this are sorted out.