Not sure if anyone mentioned it, but Mega Salamence totally has arms... it just tucks them in to reduce air resistance, which if anything adds to the quality of the design. That said, I am -not- a fan... but I also never liked normal Salamence, so there's that.
Ugliest to me... Lickilicky. I hate everything about its design. Lickitung was never the best looking thing, but it had kind of a cool salamander/dinosaur thing going, and it was almost so ugly it was cute. Lickilicky, though? They took -everything- bad about Lickitung, made it all worse, then completely destroyed the good qualities by making it a figureless blimp, slapping a wi-fi signal on it, and giving it a weird haircut. I can't even really find a proper place to break down what's so... awful here. It's just a terrible, terrible design.
Some honorable mentions...
Rhyperior: Not the biggest fan of Rhydon, but I do like it and feel it indeed did deserve an evolution... but not the one it got. Sadly, Rhyperior really isn't that far off from being a good design, they just... screwed up somehow. It no longer has ANY figure of any kind, it's just round... which makes it look lazy. It's supposedly meant to look like a construction worker, which I just find silly and kind of lame. The plates on it feel random, impractical, and just copy-pasted on. The complete lack of ears is APPALLING... and while this has nothing to do with looks, the stats are just pathetic. +10 to each stat except Speed? Really? That's ALL it gets? ALL that extra bulk uglying it up, and it ONLY gets +50 BST in the laziest, least useful distribution possible? Eesh. Strangely, none of my hatred stems from it looking very different from its previous evolutions... I actually think it matches pretty closely. I just think it completely sucked all the good out of the first two stages.
Barbaracle: I'm kind of offended it even exists. It's just one of those designs that's so ugly it makes me kind of angry to look at. It's kind of creative I suppose, but it's done in the worst possible way. Maybe if the faces weren't so... unbelievably stupid looking, that might help... but they just look really, really stupid. Nothing about this feels like it works for me.
Hoopa: Let me get this out in the open right away; I adore Hoopa Unbound. I think it has a really solid design, it's menacing, it looks legendary... it works. And because its Unbound design is SO good, it improved my opinion on the normal version. However... it's still pretty terrible looking to me. It's not cute, it's not cool, it's not even really unique. It's the worst kind of combination of 'filler' and 'ugly' design to me, and if it weren't for the Unbound version it would be my all-time least favorite Legendary ever.
Stunfisk / Garbador / Muk / Feebas: These ones are a little different, as they're INTENDED to be ugly... so mentioning them here is actually kind of a compliment. But damn if they're not some of the ugliest things GF has ever come up with... @_@
Magmortar: It's sad I've had to mention so many Gen 4 cross-evo's, because I find a lot of them to actually be pretty awesome. This, however, is not one of them. It took something that already had a "if it wasn't for that ONE thing I'd love its design" appearance... and beat it to near death with an ugly stick. All the worst traits of Magmar EXPLODE out of this in a fiery mess of ass. It's just so unbelievably uninspired and awful, like they had absolutely NO idea what to do with it but they REALLY wanted to give Electabuzz's counterpart an evolution since they'd already made Electivire.
Therian Landorus/Tornadus: Ewww... what the... I don't even... nooo, that's wrong. They both just look like bizarre, poorly drawn animals with human faces attached. There's nothing really inspired here. It's just... no. T-Landorus has a FEW qualities that I don't mind, but T-Tornadus is irredeemable. Ironically Therian Thundurus is one of my all-time favorite Legendaries.
Timburr Line: Ironically I don't find Timburr to be THAT bad, but Gurdurr and Conkeldurr are terrible. The strangest part is the veins aren't what bother me, because while those are NOT pretty they compliment the design from a conceptual standpoint. What makes them so bad is... pretty much everything else, primarily the head and especially the nose. It's like it's designed to make you want to hate it.
Tympole Line: I swear I like Generation V. It actually has many of my favorite designs in the series, but it also had some reeeeally ugly ones. This is possibly the ugliest line in the entire series, though, at least factoring in ALL stages. First of all, Tympole isn't remotely cute... it's ugly. Second, Palpitoad itself might rival Lickilicky in terms of sheer hideousness... I mean there is NOTHING good about that horrid abomination's design whatsoever, it's awful. As for Seimistoad... it's not the worst of designs, but the ugly warts and ESPECIALLY the bra head makes it skyrocket in terms of ugliness... granted it wasn't exactly pretty before.
Diancie: I feel bad for listing it as ugly, since its Mega is one of my all-time favorites and I think Carbink is precious beyond words... but ordinary Diancie is just really, really unappealing to me. The sad part is most of what I find so ugly is JUST the giant rock butt, but it's enough to completely destroy the rest of it for me. It feels so random and unpolished, like a half carved gem statue that has a lower half that's gone entirely unattended and just left raw.
Gothitelle line / Jynx line / Mr. Mime line / Jigglypuff line: The same basic description suits all of them perfectly for me, so I can't really bother separating them... they're just plain hideous to look at. Every one of them is either so bad I wish it didn't exist, or has a much better looking counterpart out there. NONE of them have a single quality that appeals to me in any capacity, and Smoochum and Gothita in particular actually anger me a little bit.