A) If I have to pay for the base bonuses individually, it seems likely that I'll be "shorted" on some of the skill bonuses that I would have under the current system. (How much would depend on the method of character creation and possibly attribute rolls.) See below. This also, I suspect, would create a disproportionate burden on the "skillsy" or "smart" classes vs the "dumb" classes. That is, replacing the skill points from a High Int (5 skills), Wis (5 skills), or Cha (4 skills) would cost more than replacing those from Con (0 skills) or Str (1 skill). This could be compensated for by making Fighting, Might (melee damage), Shooting, and even Resilience (bonus HP) into skills, but then...are you playing D&D anymore?
B) An array would allow you to specify how many skills at each bonus. So you might have something like: Choose two skills at +3, three at +2, and three at +1. That would be the equivalent of 31 points if each bonus costs one point, and only 8 skills with positive bonuses (pre-proficiency, if I understand your suggestion).
A&B) That's a significant loss vs. the current system (typically).* I might alternatively suggest that you start skills with a base of 0, and allow 3 skills to be reduced to -2 to gain further points. Of course, one could argue that the specificity of choosing the skills would be worth the loss.
C) Right you are. I was still thinking like previous editions. (Presuming you intend to maintain Ability bonuses to the relevant checks.)
*Standard array has only one ability score with a negative modifier. Potentially, that's no or only one skill(s) with a default negative modifier. Even if you "dump" Intelligence and/or Wisdom, that's still nine skills with a positive base modifier.