You're slightly misinformed to begin with.
First off, the EL is basically a luxurious Civic. If you want luxury over size, engine power, and performance...get that. But the Accord and EL are COMPLETELY different cars in just about every way.
Secondly, the Accord's transmission problems have been fixed. The 2003 model has a brand new 5 speed automatic. On other cars like the TL and CL that still have a tranny based on the Accord's, the problem has been fixed since MY 2002. But, since it's a completely new model, some problems are bound to arise. But that's why you have a warranty.
The question to you is what your perogatives are since the Accord and EL are so different. Hope I helped a little
Chris