First of all, I apologise if this has been asked before - I suspect it has, and I did do a forum search, but my powers are weak...

I've just got the core books for EoE and AoR and I've been having a read, during which I noticed that in a lot of cases there is a duplication between the career skills you get for chosing a career and those you get as extras for a specialisation. As far as I can see, there's no benefit to having a career ability twice, except at character gen when you can get two free points in it, Is that the case? If so, it seems that some career/specialisation combinations get short-changed; for instance, if an Ace chooses the Driver or Pilot specialisations they only have eight career abilities, as all four that they get for their specialisation they already have from their career, while a Gunner would have eleven career abiilities as only Gunnery is duplicated.

That is correct.

In your example above of the Ace career, both Pilot and Driver are loosing out on potential career skills, but also as you said they are gaining the option to start with two (three if a droid) career related skills at rank 2 of their choice. That is nothing to sneeze at.

The Gunner by comparison can ONLY start with Gunnery at 2. So there is a potential loss of 5 (10 if a droid) "potential" XP.

There is also nothing stopping you from starting as a Driver/Pilot and picking up Gunner early on to gain those extra career skills as well as gaining access to some good talent synergies if you are flying a fighter. After all, the 20xp from going into Gunner will be cost neutral at 4 skill ranks in Discipline, Ranged (Heavy) and/or Resilience.