I think the metagame would be a lot healthier without Deoxys, Hurricane-T, and Genesect.
Deoxys-D performs the role of a hazard setter nearly identically to Deoxys-S. The only difference is that Deo-D is significantly slower (and by no means is Deo-D slow. It's not). Deo-S was banned because there was almost nothing capable of stopping it from doing what it did best. Even now, there's nothing that can reliably stop Deo-D from setting up one or more layers.
As far as banning rain goes, sun would probably have to go with it, which I don't feel is necessary. Just by banning Tornadus-T, rain would instantly become balanced. Having literally one safe switch in (Jirachi) is pretty sad, especially considering that if Tornadus decides to u-turn out to dugtrio when you switch in jirachi, you can say bye to your Tornadus check. This thing brings too much to the table to promote a healthy OU metagame. It also almost singlehandedly (along with bff Genesect), crippled stall as a playstyle.
Lastly, Genesect. If we lived in a metagame where dugtrio didn't exist, It wouldn't be nearly as much of a problem, but because of the existence of duggy, genesect is absurdly good. As bubbly stated, it's pretty ridiculous to suggest banning dugtrio + genesect or dugtrio by itself, so getting rid of genesect makes the most sense imo.