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Let me try and get this shit straight.
What are the pros of having the Furniture mod? Lots of aesthetics. Fuckloads of it, really. It makes everything seem a bit comfier and all-in-all more enjoyable. As a big bonus, it works extremely well with Pixelmon itself for a much easier lifestyle (e.g. processing obsidian easily, easier Pokéball production, etc).
The cons? Glitches everywhere. While I said it works together well with Pixelmon gameplay wise, it has a lot of compatibility issues, with Pixelmon, other mods and even vanilla itself. Worse, these glitches can be easily exploitable by autists that don't want fun, and can cause crashes and damage to the server.
Basically; either remove the Furniture mod for less bugs and glitches, or keep it for ease-of-access gameplay. I'd say, at least for now, remove the Furniture mod (until a more stable version is released).