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I'm the one who made the concept vs execution thread yesterday you're probably lying talking about.
There's a difference between ugly and poorly-designed. Your example is Garbodor, which I believe is one of the rare cases of bad concept, good execution. There are others that may disagree with me, and that's fine.
Anyway, a Pokémon can be ugly and well-designed. I used the example of Venusaur and Magmar last thread. Magmar is not a good design; nothing about it works well together. Venusaur is a good design, as it looks monstrous and powerful without being a clusterfuck of colors and shapes.
I can think of lots of non-ugly Pokémon with a bad execution.
Bewear. It isn't ugly, it's more off-putting. Terrible execution.
Zapdos. Its anatomy makes no sense. It doesn't look like it can move any part of its body.
Roserade. One of my personal favorite Pokémon, but why oh why do the bouquets look like that?
Manectric. The design just doesn't work.
This is all opinion. You can disagree. Just understand the separation of concept versus execution. Many people don't value them equally.
Your point about Game Freak not making ugly designs is stupid. Who cares what Game Freak thinks? They've been making poor designs since the first generation. This has nothing to do with Game Freak.