I'm solidly in the 'repair beams make absolutely no sense' camp.
From realism/lore: if they have nanobots that can reconstruct complicated armor systems and hull, why do they need autofactories? Why do repairs take any time at all? It would be a glaring hole in internal consistency.
From gameplay (because realism/lore arguments are only marginally meaningful): Healing almost never adds depth to a game. There is a very fine balance between A) healing is too powerful so the only viable strategy is to attack/defend the healers and B) healing is too weak and can be mostly ignored in the heat of combat. For Starfarer, the only thing I can see heal rays doing is making the 'ball of death' strategy even better, or making small strike ships more powerful. I suppose it would be nice for mods, but I would rather have core features first.
For those interested, Alex addressed cooperative systems in the comments of the most recent blog post:
@asdfg: Right – I see what you’re saying. I think those are good ideas for system – so, let me explain why not very many systems like that are in the game (in fact, the only one I can think of is the ECM Emitter on the Omen – which, lightning-based as it is, is functionally a field around the ship where stuff (missiles, fighters, ship weapons/engines) gets disabled).
It comes down to what you’ve said in the beginning – ” The reasoning is to have a true support or “force multiplier” type roles that opens up more complex and interesting tactics/strategies.”
Now, there’s nothing inherently wrong with that – but I think these types of tactics/strategies are more naturally suited to emerging in multiplayer coop game. I don’t think it’s something the AI could pull off – at best, it’d know a few canned strategies, and the player would be frustrated in not being able to get the AI to cooperate with them how they want, when they come up with something new they want to try. A potential answer would be allowing more explicit control of allied ships, but that’s not a direction I want to go (makes the game too much of an RTS and takes away from piloting your ship).
That said, some of these could work – say, a tractor beam version of the inertial dampener. But the more purely-dependent-on-effective-cooperation a system would be, the more likely it is to run into trouble. This is exactly one of those design issues that come up if you try to design a game to have both multi and single player in it. For a co-op multiplayer game, systems that allow/force the players interact with each other are a must. For a single-player game, I don’t think it’s such a good idea – again, can be done to an extent, but shouldn’t be the focus.