Ply is better than MDF in my opinion, but they both have their places. MDF dulls tools and the dust is terrible. Finishing it is a bit trick.
As for pockets vs blocks... The strongest is glue. Like stronger than the wood it's joining. The pocket screws and blocks just hold it together while the glue dries. That said, one could just screw it together, but over the long term, it will not be as durable as gluing. Think of Ikea furniture. If you had an Allen key and tried it on every piece that you say on or interacted with and you'd find loose screws and sloppy joints. It's why I use glue on some of my Ikea stuff... So I don't need to keep that damned key!
There is no right or wrong I don't think... Just gotta go with what you're comfortable with and what you feel best meets your needs. Now if you want to angle your joysticks, I think there is a consensus there