>One dude is maintaining Forge/MinecraftCodersPack/Fernflower, which powers pretty much every mod
Forge is maintained by cpw and Lex, as well as a large community of modders. MCP is a completely different project and is still headed by Searge and ProfMobius (now with Mojang), among others. And I'm not sure what Fernflower has to do with anything.
>Ad-infested forums and adfly links are the preferred way of distributing mods
Partially true. Many have moved to Curse or CurseForge (which isn't any better).
>The last moddable client version is 1.8.0, 1.9 is out.
1.9 is not out, and work cannot even begin on enabling 1.9 mods until MCP is released. They'd be working with obfuscated code otherwise.
>Getting a mod started is really difficult, and it's not clear what should/shouldn't be in source control.
Having just recently gone through this, I wouldn't say it's that bad. It will generate a .gitignore file for you, and set up workspaces for both IDEA and Eclipse. Other IDEs may be more difficult to setup.