The gen1 pokemon were mostly based off animals and were much simpler in design. Gen5 pokemon are overdesigned. Look at Emboar for example. His black and gold markings are way too overdone to appear natural. Too much stuff in gen5 just looks unnatural.
His gold markings are there because that whole line is supposed to look Chinese in design. I had to look this next bit up, but Journey to the West is probably its inspiration along with Infernape's.
The unnatural Pokemon bit can go anywhere, because where do you draw the line for what's natural? Is Magnemite natural? It's a magnet with an eye. Is Golem natural? It's a golem, an animated rock. Ditto is unnatural in design too, it's literally a blob of stuff. I went through and picked out Pokemon in Gen 1 and 5 that are either man-made or an "animated" object just for the sake of comparison:
Gen 1: Magnemite, Magneton, Grimer, Muk, Voltorb, Electrode, Exeggcute, Koffing, Weezing, Ditto, Mewtwo, Geodude, Graveler, Golem (14/151) ~9%
Gen 5: Munna, Musharna, Roggenrola, Boldore, Gigalith, Darumaka, Trubbish, Garbodor, Vanillite, Vanillish, Vaniilluxe, Kling, Klang, Klingklang, Golett, Golurk, Litwick, Lampent, Chandelure, Genesect (20/154) ~13%
And that's not too bad, there's not even 2x the amount of unnatural Pokemon in Gen 5. We could do this by looking at every single Pokemon and its design too.
Like Teran said the shift is there in art style and what is aesthetically pleasing, but really, as far as unnatural Pokemon go, it's stayed much the same.
Metroid Prime was on GC which limited its exposure to juat avid gamers/Nintendo fans, and since GC finished last in the last console wars, you'll find that it's not something that transcends.
Metroid Prime was amazing, but talk to your average teenager or person, play some tracks to them. They'd probably recognise Mario, Zelda, Pokémon, Halo, but I don't think they'd recognise Metroid Prime's theme.
I think you're confusing "revered among nerds" with "breaking through the confines of its own demographic with its exposure". People who've never played Mario or Zelda still know the music.
Funny story, but for a small video project I needed some creepy ambient music so I immediately thought of Metroid Prime and put some forgettable theme in the video. I specifically tried to find one that didn't have any indication that it was Metroid in it. It was I think one of the Chozo Ruins themes.
After the video was done this one kid asked me if I had ever played Metroid, since he said he recognized the music. It was pretty awesome.