GRRR - I had written a reply to this and somehow - I have absolutely no clue how - I closed my browser and lost it, so I'll just do a readers digest version.
When I reached VA with my first character, I was borked like this - I had dumped points into the low-level skills and had no space to spend my last 100 points. It took me a little while to figure out I was going to have to respec. I had never done it before, so I burned up my first respec token on just getting the promotion.
I'd advise you to watch the episode of STOked, about diminishing returns, and use STOwiki and every other resource you can find to plan out what exactly you want from your character, and what kind of ship(s) you plan to fly as a VA, and THEN go and respec so you don't waste a token on just a single skill adjustment.
After I learned about diminishing returns and really paid attention to what is gained by allocating points, I stopped putting 9 points into anything that doesn't result in the ability to train an officer in a skill. The best "bang for your buck" is typically putting around 4-5 points in a skill, and doing that with twice as many skills - although if you really want to specialize and wring every single tiny bonus gain for something specific, you can, of course, do that.
I'm just approaching my 300 day vet award - I'm not an expert at this game by any means. I can hold my own in a fight (although I rarely PVP), and I haven't really experienced any of the troubles some people have had with the changes in ground combat for Season 4, which tells me I must be doing SOMETHING right. I still learn new things about this game every week that goes by, and I don't think it is possible for anyone to know absolutely everything off by heart. I've chosen to give my (playable) officers a broad range of skills with moderate point levels, rather than loading up a small number of them with 9s.
Learn all you can so that if you have to respec you only have to do it one time, even take some time to write it down if you need to. There are some sites with some great planning tools out there (google is your friend, and fleet websites, and these forums) - make the most of them.
A basic rule of thumb is to use the "7-7-9 approach". Basically don't spend 9 points in your Tier 1 and Tier 2 skills. Put 7 in those - any more doesn't provide much benefit (unless it unlocks BO training).
Then if you end up having 100 points to spend before you can be Vice Admiral, you could put it into one of your Tier 1 skills.
But if you take the time to read the above SSW Thread, *you will want to respec* to get the most out of your points and the OP's problem will not be an issue.
Is that true? That 100 point skills arent that useful? I have all of mine maxxed and if its not worth it I will sure as hell respec
While there have been some changes since this article was written, the skill system has remained similar enough that everything there is still relevant.
I never buy more than 5 levels of any 100 point skill except to get to the 6700 SP mark, and then, I don't go beyond 7 in anything else I need to spend points in. The gains are so minuscule for ranks 8 and 9, they're honestly not worth it.