The point is not that you could cap and thus have more than one elite skill on your bar. You've always been able to to that, for years. You will lose the second elite skill as soon as you zone anyway.
The point is also not to allow cap sigs in PvP. That doesn't make sense and to my knowledge it was never possible (or was it? not really sure).
Fact is, cap sigs have always had a special role. As long as I remember, it was possible to have up to eight cap sigs on your bar. Which doesn't really make sense either, but it was possible! And in some places it
does make sense to have multiple cap sigs (well, not
eight, but two or three for sure!).
Now come the new PvE-only skills, cap sigs were thrown into one pot with them. Technically, that is correct, they are PvE-only, too, after all. But what has changed at the role of cap sigs since PvE-only skills were introduced? In my eyes, absolutely nothing. So why is it neccessary for them to be limited now in a way there were not limited before? I do not see a valid reason.
Granted, things change in Guildwars, and sometimes restrictions have to be implemented to prevent abuse of features or combinations that were not there earlier. But I do not see that here. Cap sigs still have the same special role as before. They are still excempt from the "only one copy of each skill" rule. They should also be excempt from the "only three PvE-only skills" rule.
Or in short: /signed.