You should never, ever, under any circumstances attack with a skill vs. a defense.
Actually, on reflection I think they would do
much better to adjust the total skill modifiers so that they are on a par with the attack bonuses (and reduce the skill DCs to compensate).
Assuming the use of the SWSE BAB-by-individual-class and skills-gain-+1-per-2-levels, I would suggest the following:
1) Introduce a "non-proficiency" penalty of -5 for using skills untrained, equivalent to the penalty for using a weapon untrained.
2) The Skill Training feat, instead of giving a +5 bonus with the skill, instead negates that -5 non-proficiency penalty.
3) Add an Improved Skill Training feat (that requires Skill Training as a prerequisite) that gives a bonus equal to half the character's level to a specific skill.
4) Skill Focus should give the same bonus as Weapon Focus (+1?).
(The feats that give a bonus to two different skills will probably need to be eliminated. They're a bit too good in this paradigm.)
5) Be sure to reduce the skill DCs to reflect the new, lower, skill modifiers!
That way, the character's total modifier with his best skills should be roughly equal to his attack bonus with his best weapon (assuming good BAB and equal scores).
Example: Let's consider a 4th level Jedi with Weapon Focus (lightsaber), Skill Training (use the force), Improved Skill Training (use the force), and Skill Focus (use the force). We'll assume a Str of 14 and a Cha of 14, giving a +2 bonus in each case.
His attack bonus with his lightsaber is: +4 (BAB) +2 (Str) +1 (WF), for a total of +7
His Use the Force skill modifier is: +2 (half-level automatic) +2 (Cha) +2 (IST (also equals half level!)) +1 (SF), for a total of +7.
If you do this, then it doesn't matter whether the character uses an attack vs a defense or a skill vs a defense - the total modifier is in the same balllpark whichever is used. It also means we can unify the DCs for attack and skill rolls by level, which definitely seems like a good idea to me.
(If we instead go with a 4e-like unified modifier for all gains, and a proficiency
bonus for using an appropriate weapon, then Skill Training should instead give a middle-of-the-road bonus (+5 is too high), my suggested Improved Skill Training feat should be eliminated, and Skill Focus should again give the same bonus as Weapon Focus).