I doubt it. It would be impossible to get a good view of both a Pichu and a Tyranitar battling each other with accurate Pokemon sizes.
I'd rather it stay that way, anyways. I hate to think about the fact that sweet little Togekiss is almost my height. In my head, I want it to be Togetic-sized.
I will echo what other people have said, and say that it would be quite difficult to manipulate the cameras in such a way that Joltik and Wailord can fight each other without some crazy camera angles.
I do think Pokemon scaled to their actual sizes would be cool. The only issue is, from what we've seen from the trailers, I doubt that this will happen with these games (unless they change a lot of things before release day). Golurk is 9'02", and unless Froakie is like 2-3 feet tall (which I find a tad unlikely, and certainly weird) Froakie really didn't look that small in comparison.
Pichu and Tyranitar would be extremely easy to have on the battle arena (with accurate sizes) though. There's only a five foot seven inch different in height between them.
I mean, maybe it's just me being too personally attached to my Pokemon, but I'd feel bad if something like a tiny Jirachi or a really small legendary goes up against something twice it's size like Dragonite or something?? Kind of a worrying thought at first, I'd rather if they were kept to a certain standard size or something. u__u
While they'll obviously scale down some of the larger Pokémon to fit accordingly on screen, it seems as though there will definitely be a change in proportion from previous games given the screen grab below (or click to see it here).
I had not noticed this earlier from the trailer because it went by so quickly, but I definitely like this more realistic approach. It certainly adds more depth during battles.