Sure, those who ride a compact and a traditional frame will notice differences, but then again, they'd notice differences between a Giant TCR and a Airborne Torch (both compact) as well. And between a Klein Q-Pro and a Felt F15 (both traditional).
From what I've read, there's very little real data that illustrates real differences in ride quality between two otherwise equal bikes with compact and traditional geometry. Geometry matters, but in the end, compact frames offer head tube angles in the same range as non-compact frames; same for seat tubes, bottom bracket position, and wheelbase. Those characteristics, along with tube material, construction and assembly make a more significant universal difference.
The bottom line? There are great bikes made in both compact and standard styles. There are racy, twitchy non-compact frames; there are easy-riding and mellow compact frames. There are elite pro teams on both styles. In other words, don't worry about standard vs. compact -- concern yourself with the usual issues: fit, price, component selection, style, durability, and so on.
Good luck!