I've played both and I own both. Here is my critique.

D20 CoC is entertaining if you are more of a combat oriented player. Because of the fact players can easily beat the monsters with the right planning and level, I don't really like it. I mean if me and my friends who played waited till all 5 of us got to level 30-40 we could take on a good number of the Gods in the book. It just seems way to primitive and I think it failed to capture the true lovecraftian essence.... HOWEVER!
If one was wanting a lovecraftian RPG I would suggest trying the D20 CoC first just to get a bit of a background in Lovecraftian Role Playing.

Chaosiums CoC
I think it's the better of the two, it's more complex, realistic(sp) and difficult. It would take investigators a long time and a lot of blood shed to take down the average monster in Chaosium's book, and it's just full of awesome! It's way more focused on actual role playing and woe unto the ivestigator who runs into guns a blazing! Cos as Grandpa taught... It doesn't work... And to also add onto the RP experience of the Chaosium CoC try playing it without leveling your character....

Because the Chaosium CoC is more complex I'd go ahead and encourage the aspiriing RPGer to try the D20 first.