For what it's worth, here's my two (or three) cents on respeccing.
(personal opinions only coming from my own view on how I like to play games, fully appreciate other people have differing opinions, feel free to discuss / shoot me down where necessary
In games like Diablo, I can see the benefit. The storyline is very linear (at least Diablo 2 was) and once you get through act 1, into act 2 and on to act 3, you might be at a point where you are thinking you should have taken an extra point in Orthodontics or whatever, instead of that neat-sounding Synesthesia skill.
Fighting those buffed pit fiends and tasting the colour of their skin every time they hit you is no longer a benefit (it was great in Act 1 at low level), and now you have finally reached Barney the Phase Dinosaur, you really need to be able to replace all those lost teeth in a hurry, rapidly and during combat.
It's also very much a game about making a lot of decisions to build a character through a lot of levels very quickly as you advance through stronger and stronger enemies - It's about progression. As the game gets progressively harder, marginal efficiencies in character builds become more and more important to maintain an effective, and fun, character.
This linearity and progression means that it isn't necessarily fun if you get to a brick wall where 1 skill pick is the difference between being able to advance and not.
I remember getting to Diablo on Diablo 2 and my necromancer could not defeat him with my army of skeletons. The difference was literally one skill pick in getting them SOME elemental resistance (confirmed by cheating!). It would have been a 6-hour grind or something, tracing back through boring levels I could easily conquer to achieve this (going up a level or finding a suitable enchanted head). Needless to say, I dropped the game and don't think I ever returned to it at this point. In this case respeccing would have solved this issue for me, and the lack of it was a problem.
In Starfarer, I don't envisage that this will be the way things pan out. After 6 cycles, in your first game, you might be only just coming to terms with how you are wanting to play the game, and your combat build is really hampering your wish to trade as efficiently as possible. But I don't think Starfarer is supposed to be about progression, so much as ... conflict? Change?
The question is, do you allow respeccing, or encourage the player to stick it out / start a new game?
What does the sector look like after 6 cycles? What benefit would there be in the player becoming the person 'they always wanted to be', in the sector at this point? What's wrong with being a grizzled, battle-seasoned commander running a few freighters from port to port - it's still a fun exercise, even if you aren't doing it AS EFFICIENTLY AS POSSIBLE?
What about after 16 cycles when the Cult of Lud becoming a monstrous force in your main trade route, and you decide that there is more to be gained by being that legendary Commander from 12-13 cycles ago, maybe throwing your lot in with the Hegemony? Do you let people flip-flop between trades? How does this affect immersion?
I come from a background of enjoying hard and unforgiving games, like Nethack, Jagged Alliance 2, XCOM etc. and I thoroughly enjoy the aspect of 'losing' and coming at it afresh - and having to start a new game or just sitting by as the world crumbles around me (damn Ethereals). My first thought would be that respeccing is not for me.
I hope, if the world is living and breathing (even if those breaths are becoming less and less strong with each cycle) - then the majority of players will step away from thinking about DPS increases of 2%, and just playing things the way they want to play things and going along for the ride.
Having that push on players to stick with their decisions and ride them out to the end (even if that means their end) is (to me, at least) a positive one for the enjoyment of a game, and should form the basis of the 'vanilla balance' of the game.
I'm not against it if it turns out that it really does add to the game (and in truth, it probably will, as I can only imagine how difficult all the design issues will be to truly say that it won't) - but I wouldn't want it to be the default position for the grand-master-plan of how a typical game should play out.
He he ... oops, maybe that's four or five cents