Here are my top five least favorite ones:

1. Altaria: I honestly think this Pokemon has one of the worst designs. It's a full-blue bird that's mostly covered by clouds and uses said clouds as wings. I thought it looked cool at first, but then I saw it in the 3D games. It's weak, and also annoyingly bulky.
2. Bouffalant: I don't like that this thing was based primarily on a hairstyle, I think it looks rediculous. Apart from that, it never seems to die in just one hit. Did I mention that one of its attacks is called 'Afro Break' in Japanese?
3. Pikachu: I want to blame the anime for this one being on my dislike list. Particularly from the Gen 3 anime and on, Pikachu isn't devious anymore and he seems to be more whiny. I also don't like how the entire franchise is based off of just him.
4. Diggersby: I have major issues with its design. It's too fat compared to Bunnelby and its ear-arms are disturbing. It also has one of the most disgusting Pokemon cries in my opinion.
5. Burmy: I never was crazy about its design. I think the biggest issue for me was its mouth. It also looks creepy when it doesn't have any leaves on.

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I'm usually pretty positive about Unova's diversity, but I have to question Trubbish and Garbodor.

They're bloody garbage bags that are bursting at the seams.

You're joking, right?

Honorable mention goes to Pikachu (the world is oversaturated with the thing), the Lake Trio (Sinnoh had too many legendaries to begin with, and with these they didn't even bother to give them different types or abilities), Glailie (it's the epitome of "pointless") and Feebas (Milotic's a cool Pokémon and all, but they made it WAY harder to obtain than it's worth. Even in Gen V, it was kind of a pain to get one.)

I'd have to go with kirlia and gothitelle's line. I'm just not a fan of girly looking Pokemon that can be males.

Not even sure if Gothitelle's line can be male, but either way I find it very unnappealing. Oh and Aromatisse.

5. Muk
Ugly shade of purple, overall ugly. It is meant to be ugly as well, but that doesn't make it un-ugly.

4. Pyroar Female
Really not a fan. I don't like hair like that IRL either. Looks ugly.

3. Aromatisse
For taking Spritzee's potential and crushing, grinding and burning it.

2. Jynx
Ew I don't even what

1. Hoopa
Such a great type combo... such a hideous thing.

The kami trio used to be pretty low on the list of interesting Pokémon prior to the addition of their Therian formes. Oddly, I do like the lake trio.

I'm not too fond of Pokémon that are created to be useless, like most of the babies. The only reason those exist is for them to have more cuteness appeal.

I'd have more to say, but my mind has gone blank and focused on an upcoming exam.

Bronzong, whenever I see this thing I almost always loose plus it has a lazy design and it's just annoying.

Furfrou. I liked the idea of a customizeable poodle until I saw its natural look's face. It looks like it wants to rip me limb from limb for even thinking of styling it.

Luvdisc. Just, *long sigh* Luvdisc. Baby Pokemon except Pichu, for Volt Tackle), and some scattered others that dont come to mind

Heatran.
I just outright hate its design. It's an ugly as sin creature and I just despise looking at it.

5. All babies (Gen II, I'm looking at you.) What better way to promote breeding than with this useless adorable Pokémon we're throwing at you? You can get it by throwing a good Pokémon into the Daycare with a Ditto!

4. Most single stage Pokémon. I don't understand, if evolution makes things better than does that mean these are already god-like? Well they're not legendaries their stats aren't impressive, so what are they for? There are rare exceptions, like Heracross and Taurafros, but things like Dunsparce and Farfetch'd kill me.

3. The Chikorita line (minus Bayleef<3). It's my least favorite grass type, even more than Jumpluff and Sunflora. I think it's the worst starter ever and the design is just unnatural.

2. Spider Pokémon. It's obvious.

1. I hate nothing more than Garchomp. Garchomp is my ultimate weakness and it never fails to constantly remind me of that. It's the most evil dragon I've ever fought, and as Sinnoh Champion Cynthia's principle Pokémon it has been in my nightmares since I started Pokémon.

Special mention goes to Black Rayquaza for annoying me more than anything in the world.

I see some harsh words here. I think it would be polite from using labels such as "fat." Just out of respect towards human kind.

Not fond of baby forms, though I like Cleffable. If only there were done at first and not as add ons for later games. I don't like Stunfisk, either. I'm not sure why it's footprint...

I highly dislike Heatmor. I feel like it was just a waste of what another Pokemon could have been. There is nothing special when it comes to stats, moves, or design. It doesn't evolve or have a pre-evolution. I think that Heatmor is very ugly, design and color wise. The Pokemon just urks me *-_-