I have a few that I would suggest:
2nd gen:
Totodile
Bayleef
Typhlosion
3rd gen:
Mudkip
Grovyle
Blaziken
4th Gen
Piplup
Grotle
Infernape
Yes, these are all in the same format as the 1st gen. But I am sure that at least 80% of the people here will agree that the 1st evolution water types, 2nd evolution grass types, and 3rd evolution fire types all have their own really cool look/cuteness about them.
If there was some way to include all of these as 'clone-esque' types, I would be all for it. But charizard and the wings kind of mess it up. I've made some comparisons as who could easily be a clone as far as moves go.
Change withdraw to surf and all three 1st evolution water pokemon could be semi-clones.
Ivysaur, Bayleef, and Grotle could easily be semi-clones.
Blaziken and Infernape could be semi-clones.
Now I know that this will not happen, and never would, but by some chance it did... I don't think many people would mind having the different generations as "alternate costumes" type of thing. Even if they were all clones.
It would be hard to do, and won't happen. But it's a pretty unique idea.