The spawn time is not long like some have said here.
Here are my observations:
When hunting this pet I ALWAYS saw someone capturing it every time I flew through. The fact that someone was always battling one told me that the issue is not spawn times; the issue is that it is being heavily camped by many players (CRZ doesn't help), and the whelps are being taken down by someone as soon as a whelp spawn.
I decided to test this theory.
I left a character stationed there, logged in every 20 to 30 minutes, did a circle around the area, and almost every time I logged in there was a whelp, some were rare. I logged in on day two of my hunt at about 3AM server time and there where eight of them—one was a rare, but not the P/P breed I was after. I wiped out all of them except for the rares. (I called out locally for other pet hunters to get them so I could weed out the competition). The spawn of about one to three every thirty or fourty minutes was constant. I got my breed P/P in two and a half days of camping, logging in and out.
I went through a hundred Whelps in a little under three days in order to get the rare I wanted. So no, they are not that rare; they are just heavily hunted.
I would say that one Proto spawns about every half twenty to thirty minutes.
My tip is this: There is hardly ever any competition in the very early morning. I got mine about 6AM server time (but not because they spawn at 6AM, time had nothing to do with it). No one else was in the area that early, and no one ever is (except us crazy pet breed hunters), and not even someone to take the rare I didn't need that morning.
(Note: Killing dragons, eggs, and other things didn't help. I killed several eggs, whelps, and whatnot, and one solitary whelp spawned. Killing things was just giving me something to do as the time passed. When ALL the other ones spawned there was no one at all killing in the area. I didn't get mine from killing eggs and whelps; they just spawned like most other battle-pets do. If you have skinning, then killing dragons is useful. Otherwise, just log in every 30 minutes and you'll get your Emerald Proto Whelp.)
I hope this is helpful.
(Note: The character comment limit in the comments section attached to each pet is to constraining. I wanted to post my observation of the Emerald Proto Whelp spawn times with it's page; but I had to leave it on Wowhead.)