I like the idea of class skills, but I do not like how cross-class skills are implemented. What I would prefer to see is something akin to the following:
A feat that makes a skill a class skill for all classes the PC has or will gain in the future - a sort of 'signature skill' trait. Perhaps this could replace 'skill focus', in that they gain the skill as a class skill for all classes while also gaining a +2 benefit.
Another idea is to broaden class skills a bit; allow a class gained to remain a class skill hence forth:
A feat that allows a class skill from one class to be treated as class skills in another class - and vice versa. Thus a cleric / fighter would treat all class skills from both classes as class skills when they increased a level. After all, if they are multi-classing they likely are using class skills from both classes.
The former may seem like too little (only one skill is affected), while the latter may seem as too much.
Another idea I've thought on is allowing a cross-class skill to become a class skill once 4 skill pts have been put into it (granting it +2 skill ranks, the same bonus given by some feats to skills). The four points put into it show that the PC is taking the skill seriously, putting effort and skill points into it, even for only half price.
Another idea, perhaps to be used in tandem with the prior, is to remove the skill cap on cross-class skills. Since the cost is already twice that of normal skills, one can put as many points into it as they like - to the same limit as class skills (level in Pathfinder, level +3 in 3.5e). After putting in enough points for 2, 3 or perhaps 4 skill ranks, the class becomes a class skill.
It really depends on how important skills are in your campaign as to which method is better for you. If they are not too important, then perhaps allowing a class skill gained to count as a class skill henceforth (regardless from which class future levels are taken) will work. If they are too important to treat so lightly, then perhaps just removing the cap of half class skill ranks allowable is enough - perhaps even granting class level status if Skill Focus or 4+ (or 6+, or even 8+) skill points are placed into the cross-class skill.