You know I kinda sorta agree with you, some pokemon specially since the third or fourth gen have started to have a pretty wierd looking. At first i thought that the three regis looked very wierd, but then after I played the game like 5 times, i got used to them i like them, in fact its safe for me to say that i like all pokemon up to the third gen. When the fourth gen appeard, i thought they were the wierdest. But I remembered what happend with the third gen, and i said to me: unless i play the fourth gen games, i'll never get used to them. Now I have seen the complete dex and i guess I'm starting to get used to them, and some of them look pretty cool to me now, but I guess its all about that, to play the game, capture them, train them and getting fond of them, plus if you watch the anime besides the games, you'll like them a lot faster, if you like the anime of course. And if we look back to the first gen, some of them look very wierd too, like weezing, magneton, jinx, grimer... So i guess its all about that.
(SPOIL warning)Now with the fifth gen I gotta admit some of them look very wierd or exagerated, I saw a pokemon that looks just like (SPOIL!!!!!!!) an egyptian coffin, i was like WHAT?! I mean i hope they dont put an eiffel tower pokemon or terracota statue, whatever... Lets just hope they are still pokemon but its hard to imagine how it will interact or look in the anime, its kinda worrying.
But maybe its like i said you just gotta get used to them.