1. Skills shouldn't have non functional prerequisites, such as melee weapons as a prerequisite for a spear wielder who wants to get to blademaster. If this is a balance issue, just increase the cost of blademaster directly, or add a semi-functional prerequisite instead of a non functional one.
2. Reduce the amount of foreknowledge necessary for optimization. If the game is ok with me buying 3 ranks of a skill from a trainer, then paying for 3 more ranks with skill points, it should be ok with me doing this in the opposite order. If the concern is for balance, since leveling a skill up prior to paying for ranks would let you pay less for a higher level rank, either account for this in game design, or make training cost you a small amount in skill points equal to the difference between what you would have paid and what you did.
I'm not sure if that's clear... let me explain this way.
Lets say that NewSkill starts by costing 4. There's a trainer that lets me upgrade it for 500, 550, 600 in gold.
In AV5, I'll probably hold off on investing in NewSkill until I meet the trainer. So maybe I'll buy three ranks in it for a total of 1650 gold, and then pay 5 skill points to get a total of 4 ranks in NewSkill.
But lets say I've already bought one rank in NewSkill for 4 skill points. When I meet the trainer I upgrade my rank in NewSkill twice, but can't train the third trainable rank. I'll have to spend 5 skill points if I want it, leaving me at 1150 gold and 9 skill points spent.
Why not set it up like this instead?
Lets say I've already put four skill points in to buy a rank of 1. When I get to the trainer, I want to train 3 times. The cost to me is 500 for the first training, 550 for the second, and 600 gold plus one skill point for the fourth.
Now, mathematically, I'm in the same position I'd be in if I had done things AV5 style and waited to meet the trainer before investing at all. Plus I got to play with a cool skill earlier.
This can easily extrapolate out further. Suppose I had bought 4 ranks with skill points. Now it would cost me 6 to upgrade again by using skill points. If I go to the trainer, the cost would be
500 gold and 2 skill points
550 gold and 2 skill points
600 gold and 3 skill points
Still putting me at exactly the place I'd be in if I had held back from investing in advance.
See the advantages? Now I don't need a guide or multiple playthroughs to optimize my character. I can just do what comes naturally, and things work out on their own.