Should new applications still use RSA? Is it worth going down the ECDH route for protocols? I am currently designing an application for communication between two and more users. At the moment I am trying to figure out what methods to use for the asymmetric cryptology. 

With the recent "breakthroughs" that everybody has been talking about concerning RSA I am a bit unsure whether to use it or not for future projects. 

I looked at ECC and RSA alternatives such as ElGamal, but it seems like one could study that subject for the next 35 years and would still not come up with a decision. 

In particular I looked at key exchange between two or more users via a server. After reading for a day or two and striking out OTR for a protocol, I got interested in Elliptic Curve Diffie–Hellman — and as it says on the Wikipedia article: "to derive another key which can then be used to encrypt subsequent communications using a symmetric key cipher." 

However, it seems that ECDH is not advanced enough to satisfy my requirements of CIA &amp; deniable encryption with regards towards MITM attacks. 

Its suggested to use FHMQV for more advanced security. Sadly, as soon as I read the introduction I blacked out because I didn't understand anything.

I have about 1 year of deeper experience and understanding of cryptology, but I am by far no expert on this subject. 
Still, I need to make a decision and would like to know from you whether to be concerned about RSA or not and if I should go down the DH route.
Accordingly to a previous thread Why is elliptic curve cryptography not widely used, compared to RSA?, RSA is still widely used compared to ECC because:


RSA is well established
Its public key operations (e.g. signature verification, as opposed to signature generation) are faster than ECC
(most importantly) The RSA patents have expired, while a small company called Certicom holds a number of EC-related patents. 


However, according to the NSA website, Elliptic Curve Cryptography provides greater security and more efficient performance than the first generation public key techniques (RSA and Diffie-Hellman) now in use. Thus, they decided to move to elliptic curve based public key cryptography for protecting both classified and unclassified National Security information.