While it is true that if we can factor a number that is a composite of two primes is sufficient to break RSA, the security of RSA is based on a weaker property (cf. https://en.wikipedia.org/w/index.php?title=RSA_(cryptosystem...):
Given two prime number p,q >= 3, let n := p * q. Let lambda(n) = lcm(p-1, q-1) (Carmichael's totient function). A public key then is (n,e), where 1 < e < lambda(n). If one knows p,q one can compute the corresponding private key (n,d), where d * e = 1 mod lambda(n) (which is considered to be a hard problem if one does not know p,q).
The RSA problem asks that given a c \in {0, ..., n-1}, find an m \in {0, ..., n-1} such that c = m^e mod n.
It is easy to check how this problem becomes simple if we can factor n (then we simply can find the private key). But it is an open problem whether solving the RSA problem is as hard as factoring or not.
Any kind of weakness like this is bad. Especially if more vulnerabilities like this exist it gets even worse.
#1- What if an attacker was able to modify how you pick your RSA keys? You could prove that hey, this RSA key is safe, and it's roots are prime, and I just generated it. But unbeknownst to you, your attacker is cracking your RSA key as soon as you start using it. The NSA is probably already trying to attack this way.
#2- What if this isn't an isolated case, but the first discovery in an entire class of prime numbers? What if there's a whole spectrum of 'strength' of every prime and we had no idea? We need to research this topic more to find out for sure.
Problem is that it's hard to tell the difference between poor implementations and sabotaged implementations.