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The thing is, although it is a very small bonus, there are two things to consider.
1. there aren't that many Lt rank skills for you to put your points into. You will have most of them at rank 9 when you reach Lt Commander and the next colomn of skills open up to you. (or, in your case, you can probably get all of them to 7 by the time you rank up. So where exactly you spend those points at this level doesn't need to be nit picked that badly.2. This is the cheapest rank of skills. They only cost 100 per point and apply to a wide variety of places. So blowing 100 points for a .5% gain is probly not that bad. It is at the higher levels that you will want to nit pick where you spend your points on.For example. Polaron weapons. This is a T5 skill. Each point costs 500 skill to buy. If you dont use Polaron weapons, then this is a huge waste.All of the skills at T3 - T5 ranks are very specific improvements, and expensive. That is where you will really want to choose carefully. But at T1 and T2, you will probably want most every skill.
However i still don't know if 1% more bonus is better/worser than 2 extra-skills.
What you probably want to think about is whether you even want skill X or skill Y. If you want to focus on space skills, yes you may only get 1% for 200 points, but where else are you going to spend it, ground skills? That won't help your space game. This is much more of an issue as you level up, because skills get much more specific and if you don't have a BO that uses that skill, or you don't use that weapon type, then it is probably a complete waste to spend points there.
Also, keep in mind tier 1 skills cover everything. They are very general, very broad skills that cover everything in the category. Take a look at tier 2 skills. You have the same math, level 8 and 9 are 200 points for 1%. But they are more specific skills. Tier 3, 4, and 5 skills are very specific, and only affect specific weapons or powers.
So to take an example lets say you want to be really good with cannons and beams. You have starship energy weapons at 7, and cannons at 7 and beams at 7. You have 200 points. Put those 200 points anywhere and you get 1% more to something. So where do you put it? The best answer is starship energy weapons, because that gives you 1% to all energy weapons, which includes both beams and cannons, whereas if you put those 200 points in beams or cannons you only have 1% more in either beams or cannons, not both.
Also you may possibly find you have points to spare in the future, and no where to put them (not likely though!). As tier 3 4 and 5 skills are all very specific, you may find that you like a very specific BO selection so you know precisely what skills you want and any other skills are useless. You can go back and spend those extra skills on early tier skills, because putting 500 points for +10% to say, astrometrics is useless if you don't use any BO powers that depend on astrometrics.
Both your assumption and the OP's assumption that "+1" or "+0.5" to any skill immediately equates to that value modifying said skill in a direct percentage value is incorrect. Needless to say, the arguments based upon said assumptions are equally flawed.
I might refer you to Al Rivera's post about this here where he does suggest that certain skills may work in a direct 1:1 percentage ratio, but certainly not all of them. The fact of the matter is that these skills are largely undocumented and the only thing we know for certain is how additional points in the same skill modify that value in relation to less points in the same skill. Anything else is just guesswork based on user-end testing.
Therefore saying that bringing a Tier I skill to ninth rank is inefficient is largely based upon opinion more than anything else. Fact of the matter is that all Tier I skills apply broadly to a large variety of skills, and you have too many skillpoints to not raise several to ninth rank. Overall this seems like a pointless discussion.
In most of the cases I've looked at, 1 point in a skill-based stat has equated to a 1% bonus. There's a lot I haven't tested yet, obviously, but it seems like a fair rule of thumb in most cases.
I'd also humbly suggest that a hypothesis based on test results isn't the same thing as a guess.