First of all, NetBattle installs a rootkit on your computer and shoddy doesn't.
Shoddy also isn't bugged to hell and back. There are occasional move glitches, but they are competitively unimportant. On NB, so many important moves just straight up don't work (hi U-turn, Encore, etc). On top of that, when a bug is discovered in Shoddy, there is usually a team of people working on fixing it instantly.
Next, the interface of shoddy is much simpler and more intuitive to understand. In the team builder, everything is there for you on one screen, there's no navigating through multiple menus just to set EVs
On shoddy, you can also play more than one match at the same time, and there is also a clock that prevents people from taking 4:50 between every move and pissing you off because you cant just play another match while waiting.
Shoddy also came out wayyy before NB did, so there was already an established user base.
Also, the amount of barilians on shoddy is wayyy lower
NB may have other gens, but the other gen mechanics are also bugged...and not many people care about playing them anyways.
NetBattle also doesn't have a ladder
All of those objective reasons and I still havent gotten to how retarded the people who created/operate it are
There are tons of reasons to use shoddy over netbattle