I think the Heart of the Tiger novel goes into a bit more depth over Blair and Maniac's relationship.
Yes, it does. The big problem at the start of Wing Commander III is that Blair's arrival on the Victory displaces Maniac both in the ship's command structure and as her biggest war hero. Maniac had been the wing's Executive Officer and had been serving as acting Wing Commander since the previous officer's death. He had the seniority for a promotion to Lieutenant Colonel and likely expected that the job would be made permanent.... not only did Blair dash that hope, but his ordering Hobbes' back to flight status meant that Maniac wasn't even XO anymore (Blair also replaces Maniac as the squadron commander for the Thunderbolts).
More generally, though, I think the more more biting quality to their relationship has to do with the gloomy state of the war and also the fact that it must be becoming more and more apparent to Maniac that he's not going to be the big hero he always expected. Blair and Maniac had a friendly rivalry fifteen years earlier when they were invincible hot shot kids with the universe in front of them and they were given the single most desired carrier assignment in the galaxy... but in 2669 he must be thinking about the fact that he's getting towards the end of his flying years stuck in a dead end job on a third rate carrier (and is *still* being outshone by his flight school rival--essentially unbeatably so at this point).
Although it was evident that Blair thought that Maniac's style is crazy (especially in SO2), there was no hate and/or rivarly between the two.
That's interesting. The idea that there's a rivalry between Blair and Maniac was actually an idea developed between Wing Commander I and II... but it was largely introduced in the reference material. I suppose I can imagine playing Special Operations 2 without necessarily getting a hint of it. (The Wing Commander I & II Ultimate Strategy Guide was written like a novel and it focuses on Blair and Maniac's more friendly competition of the years, from the Academy through WC2. I suppose from the perspective of anyone who read that book, SO2 is a natural continuation of that story... but if not it's just Maniac being a crazy person and everyone else just feeling awkward.)
I think with many stories that run into a long "series" the writers don't seem to have planned the whole thing out from the very beginning, they make a lot of it up as they go along. Sometimes this creates inconsistencies in the characters. Look at Tolwyn, in WC2 he's a fairly basic stiff-upper-lipped, old-fashioned British military commander, but then Malcolm McDowell comes along and reinvents the character making him much more scheming, enigmatic and sinister (I find actually found him more creepy in WC3, in WC4 he was more of a cocky panto-villain)
One thing we don't like to think about is that Wing Commander III is, creatively speaking, something of a "reboot" to the franchise. The idea was to develop a game that would appeal to a (necessary, because of the cost) bigger group of people than the first two... so a *lot* of continuity is dropped in terms of story/character and things like the look (and behind the screen things like, for instance, who those 'writers' were--Chris Roberts brought in Hollywood script writers for WC3). It's a conscious choice to make Tolwyn a very-easy-to-understand bad guy instead of someone who once grudgingly won Blair's respect in previous stories, not a case of everyone forgetting what happened in WC2 when they went to make 3.
(As for how much was planned in terms of story, I know they started talking about doing a trilogy about fighting the Kilrathi after Wing Commander I was such a success... I very much doubt anything more than that.)