The prefix Y in a Group means that the car is deemed to be "better" in some way than the other cars in the base Group - typically, things like a Sun Roof or Leather Seats would be the sort of things that would count. You can't book the Y-prefix. In the past, some locations have used it to declare that they are giving out an upgrade, as opposed to going say from a B to a C Group. With the advent of Ultimate Choice, it is even less relevant than it was before.

E6 is a valid Group in its own right and is for Hybrid cars - which include the Sonata and Fusion as well as the Toyota Prius. (Group E is something completely different).

The numbers are used as there are not enough letters in the alphabet for all the different Groups, as some of the "reserve this exact model" cars have a Group all to themselves.

As to the original question, there is no definitive and single hierarchy. Upgrades and indeed car allocation always were influenced by availability. So, if you had a Group C reservation, and there were few F models (the next one up, size wise), but the place was well-stocked with SUVs, you would get a Q or Q4. But sometimes, you would get that as an "upgrade" from an F, as well, as there tend to be very few G class cars on fleet. Hertz will usually try to ensure that if you have reserved a particular body style like an SUV or a Convertible that you get one of those. so you would be unlikely to get a G or I (Luxury Car) if you'd reserved a Q or L (SUV). But every principle has its exceptions, as judgement and availability have a bearing here. Numerous threads on Ultimate Choice suggest that what gets put where can vary quite widely even by time of the week at the same location let alone between locations. Again, it is down to what they have, vs what they have booked.