Security: Binary fields has more attack vectors than prime fields
The Discrete log on ECCs with the binary field is not broken. That is not the reason. Bernstein said;
the security story for non-prime fields (e.g., binary extension fields) is more complicated and less stable than the security story for prime fields, as illustrated by 1998 Frey, 2002 Gaudry–Hess–Smart, 2009 Gaudry, and 2012 Petit–Quisquater.
As a result, choosing prime fields reduces the attack vectors, so there are fewer concerns for security.
2002 Constructive and Destructive Facets of Weil Descent on Elliptic Curves
In this paper we look in detail at the curves which arise in the method of Galbraith and Smart for producing curves in the Weil restriction of an elliptic curve over a finite field of characteristic two of composite degree. We explain how this method can be used to construct hyperelliptic cryptosystems which could be as secure as cryptosystems based on the original elliptic curve. On the other hand, we show that this may provide a way of attacking the original elliptic curve cryptosystem using recent advances in the study of the discrete logarithm problem on hyperelliptic curves
2004 Index calculus for abelian varieties and the elliptic curve discrete logarithm problem by Pierrick Gaudry
We have shown that asymptotically, elliptic curves defined over small-degree extension fields are weaker than those defined over prime fields or large prime-degree extension fields.
2012 On Polynomial Systems Arising from a Weil Descent by Christophe Petit and Jean-Jacques Quisquater
They have looked at ECDLP on the binary extension field and show that their algorithm outperforms the generic discrete logarithm algorithms for $N >2000$. The recommended sizes are not affected, yet!
Patents of the Certicom ( and others)
Another important issue is the patents that mainly the Certicom has/had.
First Bruce Schneier's quote
"Certicom certainly can claim ownership of ECC," Schneier told us. "The algorithm was developed and patented by the company's founders, and the patents are well written and strong. I don't like it, but they can claim ownership."
- One of the patents of the Certicom was about efficient $\operatorname{GF}(2^n)$ multiplication in normal basis representation; U.S. Patent 5,787,028. This patent granted in 1998 and finally expired in 2016.
- NSA had some patents on $\operatorname{GF}(2^n)$, too; [1] [2] [3] [4], however, they are expired much earlier since NSA did not paid the fees ( I think that was deliberate)
Current stage of the attacks to compare
If we look at the Certicom's ECC challenges
- A Koblitz curve over $2^{108}$ is broken in 2000.
- A $109$ bit prime curve is broken in 2002.
- A curve over $2^{109}$ is broken in 2004.
- 131-bit Binary or Prime challenges are not broken, yet.
Apart from these challenges;
- 117.35-bit elliptic curve discrete logarithm problem on a binary curve is broken in 2016 by Bernstein et. al