1. Reborn since E18 came out and the new content should keep you pretty busy, might even be worth a new playthrough since it's been a few years.
2. Insurgence since it's actually complete and is pretty good overall, has a darker plot as well. Need to finish it myself but E18>Insurgence right now.
3. Rejuvenation is very good and IMO should be above insurgence but it's not done yet so I'll slot it below the Insurgence.
4. Desolation, I'm behind on that by....I wanna say a year but it was damn good.
5. Pokemon Spork - Spork is amazing for the memes and dankness but the story is pretty good, and the "CHOOSE ANY STARTER" thing is niiiiiiiiiiiiiiiiiiiiiiiiiiiice.
6. Pokemon Uncensored - If you want a dark pokemon game set in gen 1 with crude humor this is the game for you. 100%ed and I have almost no regrets about it.
There's also Phoenix rising that just came out but that was kinda light on content and while it was good it's nowhere near done, I'd say go for a complete game if you prefer so you can dive into Rejuvenation, Desolation etc at a later date with more content to make that playthrough more fun.