I can't speak for the eCPPT, but I have taken the GPEN and from the eCPPT trial module I've looked at, and the course materials, I'd go with your assessment, eCPPT appears more 'full pen test', but GPEN appears more professionally laid out.
Are you doing this to get another job or for your own interest? If it's for a job I'd recommend the GPEN - the SANS courses are well known by management and engineers alike, so you're more likely to get a job with that qualification.
If it's for your own interest, I'd struggle to recommend the GPEN because it's not very 'hands on' at all. I went through the entire SANS SEC560 without doing a single hands-on exercise and still passed the GPEN with 95% just by answering the most logical questions and remembering some command-line arguments.