I think there is general agreement on what someone needs to learn to dive: One must be able to clear a mask, retrieve a lost regulator, share gas with a buddy, achieve neutral buoyancy, and remain generally calm. You have to understand Boyle's law at least to the degree that you realize you add air to a BC when descending and let it out when going up. You have to understand that you will use your gas faster at depth, and that there will eventually be some nitrogen-related limits to your diving. It's probably a good idea to have some idea of navigation, and to be able to get out of your gear on the surface (since many tropical dive operators require this).
Given that the core set of skills will be quite similar across all agencies (because diving, after all, is diving) then the differences in classes will boil down to the length of the class (how much pool time, how many OW dives), the standards to which students are held to pass, and the caliber of the instructional staff. Honestly, to my knowledge, among the "usual" agencies, very little in that list is controlled by the agency. The required skills must be taught to a standard which is deliberately left somewhat vague, and there may be absolute minimums set for in-water time, and some control over the order in which skills are introduced, but the class schedule is usually up to the shop or instructor, and when an instructor is satisfied with the student's performance is quite individual. In fact, the diving skill and experience of the instructor, and his teaching ability, can be extremely variable. For these reasons, it's really difficult to say any one agency's classes are reliably better than another's.
The only exception to that are small agencies which have retained intense control over their curriculum and their instructional staff. GUE has already been mentioned as one of these. There are several other agencies which are similarly small and state a commitment to diver quality (UTD, NASE) but I don't personally know all that much about how they operate or control their quality. I do know that, if you are going to mandate a longer and more demanding class, you are going to have to charge more for it; and if the process to become an instructor is similarly grueling, that instructor is not going to teach for the $50 a student which is what instructors in the Puget Sound region get for their OW classes through shops.
As much as I am a fan of GUE, the organization and its training, I don't think you have to start with GUE to get a reasonable OW class. You DO need to work with a shop or instructor which is not trying to minimize the time invested to try to improve profits. You DO have to work with an instructor who can, himself, dive reasonably well, and who has some ability to teach, and has remained inspired by teaching (burnout is a problem with diving instruction). That instructor has to have a vision of what a "diver at that level of training" should look like and be able to do, and that bar needs to be set high enough to turn out a diver who is comfortable and reasonably competent, and has a really good mental image of what good diving looks like, and an understanding that it will take practice and some application to be that diver.
Finding that needle in the haystack of dive instruction is a challenge. But those folks are out there.
