In my opinion, the biggest reason is a few somewhat irrelevant factor and mechanincs.
1. The "I hate xy thing" bandwagons. I read here an answer's comment wich mentions these ‘Hate Garbodor!’ and 'Hate Fire/Fighting starters!’ bandwagons, wich are kinda dumb of course, but there's probably a reason behind them, see the second point.
2. The reason of the previously mentioned bandwagons. If we check a few Unova pokémon, it turns out there's a bit too many of them based on inanimate objects (compared to other generations), and most of them are totally the objects you didn't expected, and the creators probably thought "there's anything can be a pokémon!" For example: Vanillite/Vanillish/Vanilluxe (ice cream), Trubbish/Garbodor (thrash bags *insert facepalm here), etc.
3. Minor pointless logic. For example, Golurk can learn Fly (how and why? *insert double facepalm here), Durant has Truant as Hidden Ability, and Deino evolves into Zweilous at level 50, then into Hydreigon at level 64. The only reason why I'm mentioning Hydreigon's evolution, if you noticed, none of other pseudo-legendaries reach their second form before level 50 and final form before level 55. And most of all pseudo-legendaries' first form could be caught between the middle and the end of the game. But Deino (in B/W) and Zweilous (in B2/W2) is only obtainable on the Victory Road! So probably these are the biggest reasons why Hydreigon is the (probably) most unpopular pseudo-legendary. And yes, Hydreigon's evolution level, growth rate and obtainment annoyed me the most, wich are absolutely nosense.
Well, that's my list, feel free to expand it with your other reasons! ;D