Confirmed that transitions do NOT lag on my iPhone 5s. You can easily make a fade in/fade out transition that doesn't involve "screenshots" yourself (perhaps you could even make such a subclass of
CCTransition and then contribute it to the community). For the other types of transitions, using "screenshots" seems to be the only option (and the older "default" transition implementations used them as well).
In any case, I have moments in my game where I am rendering two full-screen render texture "screenshots" per frame for use in a shader, and I'm getting 60 fps on every device, including iPad where it's most expensive. Perhaps your lag problem doesn't lie with
CCTransition and its use of render textures, but rather with the overhead from loading your new scene, textures, CCBs, etc. (Since the new scene is loaded into the background before the transition begins, there will certainly be an apparent hiccup before the transition begins if this is the case.)