I like Alternity, but it could stand a little cleaning up. You could remove a lot of the complexity from the system by just jettisoning the class system and making a couple skill changes.
Here’s what I’d do with an Alternity Second Edition. I’d keep the general skill basis and skill check mechanic with the differing quality of results for skill/half skill/quarter skill. Really the main rules are great and need little tweaking; the optional rulesets are where things start slipping.
Remove classes. They give you so little that it’s annoying – go “full GURPS” with it. Removes one chunk of useless complexity.
Remove levels. Spend XP as you get them. Removes a second chunk of useless complexity.
More skill points. Or cheaper costs. Definitely use at least the “Optional Rule Set 2” skill point values and, since you’re getting rid of classes, maybe just reduce all the skill point costs by one off the bat and tweak from there; maybe another one point drop for all broad skills. “But I always suck” is the main Alternity critique one hears.
Damage and hit locations. This would go a long way to fixing the armor issues. Top Secret/S.I. had a hit location/box system I really liked. You’d do this, fix the “lower number of mortal points” problem and the O/G/A weapon vs armor thing to be nicely symmetrical.
General guidance. There are a couple recurring pain points that are more about how you run the game than the rules as written. This includes “let any relevant skill work, with a 1 step penalty if it’s a real stretch.” Looking to stop a security computer on a starship from sending an alert signal? Yes, you can use Sec/Security Devices, Tech Sci/Juryrig, Computer/Hacking, or System Ops/Communications. Not “No, that’s not the perfect one.” Cover and stuff, it’s worthless currently, need a bit more focus on the firefight.
Consolidate and simplify. No separate GMG with rules players should know hidden in it. No “weapon accuracy by range modifier” special table. Make it so grenades work faster. Mainly look in the GMG, pull out all the tables, and then delete 99% of them as pointless cruft.
Psionics. Done once in the mainbook, redone in the Mindwalkers book, still sucky. Our party psis are always really weak – you don’t want to make them uber but currently you end up feeling sorry for them.
Computers. Are tarded. For what should be a sci-fi high tech game, the equipment and especially the computers are boring and stupid.
That’s it really, mostly a “delete all the exception stuff” rampage, and you’d have a terse and solid ruleset. More on specific new rules I’d like to add tomorrow…
Geek Related 
Interesting viewpoints here.
For Alternity 2.0 idea, Im just sitting back and seeing what happens with it.
Remove classes: This is a good method if you have a strong idea of the type of character you want to portray, otherwise you’re stuck looking at a bunch of skills and points and thinking “Okaaay, I have no idea what to build”. Still, im not against either concept.
I agree on the levels, or you can just bundle them up and purchase larger attributes or skills.
The more skill points problem I can see especially if only starting with one or two characters from 0-level. This is somewhat offset by the optional rules you mentioned and with a larger party where each member takes skills that appear weak on the other players’ sheets.
For armor and hit locations, I dont have a problem with it. There was a topic earlier in our forum where mortals are easily elimated versus armor becuase mortals represent vital shots or hits and guess what area of the armor has the best protection?
I like your view on the General Guidance part.
No comments on the rest other than I like the accuracy modifiers versus range. I never used psionics and hardly used the computer rules.
Yeah, I don’t think the classes help one bit in terms of character concept. The sample careers are probably better but even more ignored. (Similarly, Chapter 7: Attributes is a waste of space, designed for those who need a game to explicitly tell them their character might want to have one or more personality traits).
The paucity of skill points is one of the recurring complaints about the game. Right now, our level 11 or so party often all looks at each other and realizes no one has the right skill for a situation – not because we’re not diversified, but because it’s just not possible for characters to buy enough broad skills even to get all the bases covered.
Maybe it’s me getting old, but I have no patience for parts of games that are not a huge contribution to the gameplay – if they are not super core, cut them, that’s why we have a GM and aren’t all playing computer games. Then the core rules can actually be accessible and easy.
Maybe I’ll actually take a shot at cobbling together an Alternity 2.0. Mechanics can’t be copyrighted, and what do they care anyway. They’re too busy raping D&D’s corpse over there to worry about IP they trashed in the first place.
What would a good pseudoclone/retroclone name be for “Alternity?” Would be nice if it started with an “A” and had the same sci-fi feel. Or maybe riff on stardrive and just link it closer to that. I can think of some “alt.net” kind of stuff though that has more of a computerey feel than Alternity usually subscribes to. Aeternity? That’s used for a suitably large number of other things that no one can claim it.