I guess I'll start with what I consider the major changes I've made:
Blaster, Heavy-Weapons, Archaic Weapons, yadda yadda yadda. I've lumped most ranged hand-weapons into a single skill called Marksmanship. Yes. I know that the physics of firearms is different from those of blasters. There is recoil, muzzle-climb. Even firing a rifle is different from firing a pistol. But when all is said and done, you're still looking down the length of a weapon and lining up your shot. According to the official rules, a person with a 10D blaster skill—making him one of the best shots in the galaxy—would be as inaccurate as any novice if he picked up a slugthrower. That just never made sense to me. When you throw in Star Wars' cinematic style, I've found that I don't want to get too nitpicky. A gun is a gun. However, I have included a kind of 'familiarization' caveat to this. How it would work is: if you have a character who has definitely never fired a certain type of weapon before (say, Stormtrooper trying to fire a musket), they would have at least a -1D penalty to do so—until such time as they were able to get more familiar with it. Once familiar, the character would use their full marksmanship skill. In general, I don't make a player pay any experience points for familiarization—just time (though if you had players who might abuse this, then you could consider a 1xp cost).
I have lumped the Lightsaber skill into this one. Considering the vast array of weapons supposedly covered by the Melee skill (knives, whips, axes, swords, etc.), a lightsaber doesn't seem to be THAT specialized of a device to warrant its own unique skill. And on the flip side, I find it difficult to believe that all the dueling skills a Jedi develops don't cross over at all to other hand-weapons. So basically, Lightsaber is another familiarization (see Marksmanship above) within the over-arching Melee skill.
Other combat skills:
Thrown Weapons likewise encompasses all kinds of things, from knives to darts to grenades to rocks. And again, familiarization could come into play.
One of the things I never quite liked in the 1st or 2nd Edition SW RPG was how they handled this skill—mainly, because it didn't mesh with certain things they said and showed in the movie. First of all, Luke was a T-16 pilot, and through the movie and novels that seemed to suggest that it would translate directly into Fighter piloting. In the rules, however, they were two separate skills: Repulsorlift Operation for speeders, Starship Piloting for fighters. This got further broken down into THREE different skills in the 2nd edition: Starfighter Piloting, Repulsorlift Operation and Space Transports. This REALLY didn't satisfy me, because now it meant that Han Solo (who was a fighter pilot in the academy) wouldn't have gotten any synergy at all from that training—i.e., he'd have to start all over again with his Space Transports skill. Again, I realize that the physics of each of these things WOULD be very different. But again, in a cinematic game, I prefer to overlook them. In my game, Piloting covers a wide range of vehicles—anything that 'flies' (as opposed to low-level repulsorcraft that ARE dependent upon the ground and terrain). As with Marksmanship above, familiarizations come into play once more—for instance, your typical 'modern' star wars pilot may have quite a learning curve if he's put behind the controls of a helicopter or other 'archaic' craft.
The distinction I /did/ make as far as piloting goes was the addition of the Helmsman skill (replacing Capital Ship Piloting, I believe). While airspeeders, starfighters and transports like the Millennium Falcon all seemed to 'fly' in the same manner—larger ships seemed to have quite different maneuvering characteristics—i.e. they handled more like 'ships' than aircraft. The Helmsman skill, therefore, covers any ship larger than your basic transport (generally that means anything longer than 50 meters). The familiarities with this skill would basically be broken up into different size classes: Corvettes, Frigates, Cruisers, etc.
Other Vehicle Skills:
As with piloting, I lumped various skills together based on the general 'kind' of craft rather than its propulsion. Therefore, the Driving skill covers landspeeders, ground cars, treaded-crawlers, etc. The Cycle skill covers speeder-bikes, ground-cycles and swoops (which, though basically an aircraft, still handled more like a cycle).
This is the area I am still working on tweaking. On the one hand, I like broad 'category' skills—like a 'Mechanic' skill that would cover fixing vehicles and other primarily 'mechanical' devices. This would go along with a 'Systems-Tech' skill which would cover all primarily 'electrical' devices. But having just two skills govern the wide array of technical specialties is just too generalizing. So this is what I've come out with. I have two main branches of tech skills: Mechanical-Tech and Systems-Tech. Each of these is a skill in and of its own right. They represent broad-based knowledge of mechanical and electrical systems respectively.
A person could use the Mechanical-Tech skill to attempt repairs on anything from a landspeeder to a star destroyer (as long as it was a primarily mechanical system). HOWEVER. Since it is generalized, a person would suffer a -2D penalty when attempting to apply this general knowledge to a specific area. I have also limited this catch-all skill to a max of 6D. Meaning that at 6D, they would essentially have a 4D skill level in every different skill related to Mechanical-Tech. So what we have here is a skill for someone who wants to be a Jack-of-all-trades. Your typical handyman. If they truly want to become an expert in something, they would have to buy up individual skills related to Mechanical-Tech: i.e. Speeder-Tech, Starship-Tech, Walker-Tech, etc.
The same would apply to Systems-Tech. You could buy it up to 6D to get broad knowledge of electrical systems—but if you wanted to be an expert at something, you would have to specialize in Systems-Tech related skills: i.e. Computer-Tech, Droid-Tech, Sensor-Tech, etc.
I had considered (and am still considering) doing away with the 'general' Mechanic and Systems Tech skills and just having the others be 'Cascade' skills, but I'm not sure if I like that or not. How THAT would work is, say you have a Computer-Tech skill of 6D. Since that deals with repairing computer systems (not programming, which is a different skill), it would allow you to attempt repairs on other systems—like Comm-Tech (communications), Shield-Tech (shields), Droid-Tech, etc. At first, I was thinking it would only be a -2D penalty for these related skills, but... that doesn't seem to work either. You could get up to 8D in one tech skill and be an expert in just about everything else (6D)...it may work better if your chances with other skills were one-half your main skills: i.e. an 8D Computer-Tech would have an effective 4D skill to repair other systems-tech skills.
So, as you can see? My.. skill system is still in flux. Yeah. Maybe should have thought of that before making this post, but... meh.
In closing, I would like to talk about a game mechanic that I am still wrestling with. When first presented to me, I was...cautiously open to the idea of specializations within a particular skill. But the more I got into it, the more I disliked it. First of all, the definition of a specialization was vague. In some cases, it was like "Blaster Pistol", which made sense. You were a pistolier rather than a rifleman. Alright. But then I started seeing things like specializations in a specific type of pistol. And that seemed just too narrow. Likewise, there were some specializations that just didn't make any sense to me—like being able to specialize in dodging energy weapons versus dodging projectile. That is just a ridiculous idea. I always saw dodge more as a 'luck' kind of a skill anyway. You train/practice in moving fast, keeping low, etc. I don't think there is THAT much difference between a slug or a blaster bolt where one type of training would be more effective than another. And finally, I think my biggest problem with specialization is that I like well-rounded characters, and see specializing as (ultimately) a waste. Because you're bound to run into a situation where you have to use something other than your one special weapon or vehicle, then you're just SOL.
If I DO allow it, I think I'd have to do it kind-of like the cascade system above—other specializations within one skill would be usable at one-half the level of the specialized skill.