You can, but there'd be only four of them-- the odds of that actually working efficiently is severely low in contrast to the severely high cost of Flagstones. Sure, you can toss down a new Flagstones and thin your deck out by one single card, but it won't happen very often, and the benefit is very small. Play Flagstones, and it works like a regular Plains. Play a new one, and you can search for a Plains card (in which the only real legit reason I'd ever consider this is for dual lands), and the old Flagstones is nuked. You literally did very little for the exact same board state you would have had playing two regular old Plains, Ghost Quarter it, and you go from having 2 lands at your disposal to 1. It just doesn't translate to the $25+ cost for each Flagstones. If it was a $1 card, I'd run it for the tiny advantage. But it's just not a good card, unless there's something I'm seriously missing here.
Meanwhile, Windbrisk Heights will *always* thin your deck by a card by essentially letting you scry 4, pick the best of the 4 and set a trap with it, and put the rest on the bottom of your library. Sure, it may backfire occasionally, but the card you hide underneath will almost always be a beneficial card, because the ones you especially want to see are Spectral Procession (4 in deck), Honor of the Pure (4 in deck), or Archangel of Thune (2 in deck). If 10 possibilities aren't enough, then other acceptable cards are Ranger of Eos (I'll be running 3), Aven Mindcensor (2 in deck), Squadron Hawk (4 in deck) or maybe even Ajani's Pridemate (4 in deck).
Spectral Procession gives you three flying creatures and that also means 3 life gained times the number of Sisters on the board-- and that many more +1/+1 counters on Ajani's Pridemate or on EVERYONE if Archangel of Thune is out.
Honor of the Pure is a great bluff that lets you swing in and cast it at instant speed, obliterating weak things that the opponent blocks with.
Archangel of Thune is the best bomb in the deck, as previously mentioned.
Ranger of Eos can be cast for half price with Windbrisk, and you can thin your deck by two choice 1-drop cards with it. Deck-thinning and advantageous, especially if you've got a fairly large hand and fetch Martyr of Sands and Serra Ascendant.
Aven Mindcensor can be flashed in at the end phase for 1 mana less, because that is generally when people fetch their shock lands before their own turn so they can play it without paying 2 life. Throwing Aven Mindcensor out of Windbrisk would have you watch them blow up their fetch land for 1 life, and then be unable to search for the land they want if it's not in their top 4 cards.
Squadron Hawk is another deck-thinning ambush that gives you fuel for Martyr of Sands or at the very least, some fliers you can cast in following turns to use for whatever necessary purposes. That's more life, more damage, more chump blockers, and more power for Ajani's Pridemate if he's out.
Ajani's Pridemate is best as a last resort and you didn't get any of the above. Pridemate is super-vulnerable early game if you don't have Sister support to get him out of bolt/stat reduction removal range. Play him at a later time and he'll be much more likely to survive. And as the Soul Sisters equivalent of a Tarmogoyf, you want him to survive.
Meanwhile, Flagstones lets you rarely thin your deck for a single card for no real hand advantage or board state advantage, and very little card advantage by minuscule thinning. That is far more useful in a multi-color deck or a deck running Landfall stuff.
