I'm wondering why the checker doesn't include a check for ribbons. Take this: https://www.pokecheck.org/?pk=2362804 , for example. It has several GenIII-only ribbons despite it being obtained in GenIV, not only that it has several Battle Tower/Frontier medals despite Mew being unable to compete in it. Yet Pokécheck says it's ok. Those kind of things would be easy to look for, though I do realise my next suggestions will be a bit harder
There's also "suspicious" (yellow text) things to look out for, but it's a bit harder: for example a Pokémon having the "master" rank medal in 2 or more contest categories would be suspicious - as it's hard to max out 2 stats. Indeed you can even look at the contest stats to see if it has a high stat in a category it got a master rank medal in. Contest stats are still in GenV you just can't see them. If you Pokétransfered a Feebas with max beauty and leveled it up it still evolves. Another thing to look for here would be the fact that for it to have any contest ribbon, it also needs the ribbon that's ranked below it (ie, a pokemon with a genIII master ribbon also needs hyper, super and normal of the same type. without hyper it couldn't compete in master, without super it couldn't compete in hyper, without normal it couldn't compete in super)
For GenIV pokes you check for ribbons removed in GenV, which were presumably removed because they were never used. There are other ribbons still in the code that bulbapedia claim have not been made avialable, http://bulbapedia.bulbagarden.net/wiki/List_of_Ribbons_in_the_games . They'll be hard to verify whether or not they have been made available, but stuff like "World Champion Ribbon" should at least be considered suspicious.