The circuit design and transformers have as much to do with the sound quality of an amp as the choice of tubes. EL34s are widely beloved for their midrange qualities and the KT88s and 6550s have a reputation for a gutsier sound with better bass. But there are exceptions to any rule of thumb.
I've had several EL34 amps (the most recent a Conrad Johnson MV60) and several KT88/6550 amps. Currently I have an Image 65i with 6550 outputs and prefer it on almost all counts to the CJ I had previously.
However it is very difficult to talk about a topic like this in generalities. It will always come back to the following advice: you need to try the amp you're considering in your system, preferably under circumstances where you can compare it against your current amp or whatever the other contender happens to be.
I've had several EL34 amps (the most recent a Conrad Johnson MV60) and several KT88/6550 amps. Currently I have an Image 65i with 6550 outputs and prefer it on almost all counts to the CJ I had previously.
However it is very difficult to talk about a topic like this in generalities. It will always come back to the following advice: you need to try the amp you're considering in your system, preferably under circumstances where you can compare it against your current amp or whatever the other contender happens to be.

