I have a fair amount of amiibo myself.
The only amiibo I actually pre-ordered were the ones in the retro pack which included R.O.B, Duck Hunt Dog, and Mr. Game and watch. I regret it now that I didn't take advantage of the pre-orders when they were available.
It's true that most of them are rare and will never get a restock in store.
The method I use now to obtain them is surfing online (mostly eBay) and finding good prices. Sometimes you get really lucky and find rare ones for a fairly cheap price, which is always good.
I'm still on the lookout for ones I don't have such as, gold and silver Mario, Lucas, Wii fit trainer, and most of the newer ones.