I too first thought that Shellos was a pre-evo for Lapras.
There seems to be a connection between Luvdisc and Alamomola now that you mention it... never thought about it before though.
Cloyster looks like a Gastly hiding in a shell. :P Also, Clamperl could've been a baby Shellder.
Aaand yup. There's the Venonat -> Butterfree and Baby Kangaskhan -> Cubone/Marowak thingy. Weren't they meant to evolve like this? At least Venonat was supposed to evolve into Butterfree when they first planned it.
There's certain sameness in the shape, size, and "hairstyle" of Vanillite and Castform.

Speaking of Castform, I thought that the sunshine Cherrim is going to be a new form for it when I first saw a picture of one...
And yup, the "Pikachus" of each gen of course resemble each other. The same way I think Audino resembles Minccino. Could be their third form in my opinion, if you think of only appearance. Sylveon also has this certain Audino look.
Seismitoad looks like it would evolve from this new starter guy, Froakie.
Throh and Sawk seem related. Doh.
Petilil and Lilligant have both something "Ralts-ey" and "Vileplume-y" in them.
One would think that Shelmet would evolve into Escavalier and Karrablast into Accelgor, but they don't, and that's their thing. Pawniard and Bisharp also relate to Escavalier's and Shelmet's appearance.
Heatmor and Heatran are like brothers.
Durant makes you think that it had something to do with either Spinarak or Joltik line. Or actually, maybe Nincada!
Some Sawsbuck look like they could be members of the Swords of Justice. I also thought that Sawsbuck was going to be Stantler's next stage.
Golett and Golurk remind me of the Legendary Golems.
I bet there are others, but just some that come to mind. Some clearer than the others.
And finally my take on the Tauros -> Bouffalant thing. Yeah, species can change, so I'd have no problem with it. Similar looks are enough, and sometimes even they don't matter that much.