It's a rich and versatile system. I run my own Star*Drive game on the d20 system, which has a number of advantages, but is in a lot of ways a much flatter, more sterile engine.
Among the things that were better in Alternity:
Cybernetics. d20 Cybernetics is balanced, where it is balanced at all, by a number of suggested methods, which adds to the work of the GM, and has more the feel of buying magic items than of augmenting your physical body.
Gridrunning. d20 Cyberspace is a somewhat shrunk down version of miniature combat, which is useful, but you have to write the software you're going to use after you drop into cyberspace. Of course, Alternity used the silly but gamable principle that software was something you had to buy or program and could somehow not copy. I don't believe this will ever be the case, but at least you can drop into VR with your deck fully loaded. You could also tweak and customize your hardware, nanocomp and gridcaster, and buy advanced versions of your software. I have adapted Alternity Gridrunning rules to d20.
Skills. The skill system is richer. You can start out an expert in something, instead of expertise having to wait for higher levels. Mind you, with most DCs in d20 Modern being around 15, it doesn't take you too long to be good enough most of the time.
Starships. Starship creation rules were far superior. d20 treats dumbing down as a virtue. Sometimes it is, but in Alternity you have a lot of options to tweak your ship, its software, its accessories.
Science. If you like some science in your science fiction, Alternity had it in spades. d20, not so much. Alternity gear descriptions talk more about how the technology supposedly works. Alternity has the G.R.A.P.H. system, which rates environments by Gravity, Radiation, Atmospheric (inert, breathable, poisonous, ect.), Pressure and Heat. Armor is rated according to what environments it protects you from. Aliens are given environment ratings according to the G.R.A.P.H.s they can live in. Aliens are also categorized according to their biochemistry. Humans (and PC races in general) are Series I (water, oxygen, carbon), whereas Silicates are Series VI (sulfur, sulfer dioxide, fluorosilicone).
Some of the disadvantages of Alternity include:
Character creation requires a lot of number crunching. Different skills have different costs per rank, which must be looked up.
Four different damage tracks. Not so terrible for the player, but when the GM is keeping track of a number of enemies, it can be a big headache to determine who is at what wound level and what the effects of it are.
No miniature rules. You can work with miniatures in Alternity, and I have, but it's not native to Alternity's mechanics.
Too many skills. You can easily end up being way over specialized and useless for a module that didn't take your particular character build into account. The d20 system is kind of silly in how one skill like Knowledge (earth and life sciences) equally qualifies you to call yourself a micropalentologist or a xenonecrocrystalographer, but I'd rather have that than have a player generate a scientist who is useless for the vast majority of science rolls that might be needed in an adventure.
It's no longer supported. Actually, that's not a big deal, because they put out so much stuff for it when it was a going concern, and the books are constantly available on eBay. You can buy a supplement a month and it'll be just like having over a year of the best supported Science Fiction RPG ever.