To be honest, I agree, it wouldn't be done often but it seems hard to believe that it would only ever have been done once. But here are some reasons why it wouldn't happen often.
Not everyone would have had access to the spell.
Up until Miss Calendar got involved, it seemed as though the existence of this spell maybe wasn't even widely known outside the Roma, and certainly the actual instructions hadn't been translated into any other language. (You'd think this would have been done before. Maybe the writers thought that Romani was an extinct language. I'm told that it's not.) Once Willow and Giles had an English translation in handy word-processed format, though, you'd think they would have circulated this "lost" spell to every magician they could think of, in case it was ever needed again.
Orbs of Thesulah.
The spell also requires a special charm called an Orb of Thesulah. These didn't actually seem to be that rare. Miss Calendar went down to the Sunnydale magic shop and asked the shopkeeper for one and he had one. In fact, possibly several - he said there was no demand for them and he'd sold a couple to New Agers as paperweights. Giles later turned out to have one that he was using as a paperweight. Still, the need for an orb for each vampire would limit using the spell en masse, especially if the orbs aren't re-usable. But there might still be cases where it would make sense to try it on one particular vampire. From a purely strategic point of view, there might be a leader, say, who was too much for the hunter to tackle in a straight fight, maybe they couldn't even get at them, but this spell can be done at a distance. Or perhaps a magician had had a close friend or relative turned and was determined to try and rescue them.
Say somebody had access to the spell and the orb. There are several things that could go wrong that might put them off trying.
- Spell accident. Giles said that the "Rite of Restoration" was quite an advanced and dangerous spell, one he wasn't happy about a novice like Willow attempting. Yes, Willow did, in the event, pull it off, but as sarge_smith said in their answer, Willow was always particularly talented at magic - as witness how jealous Amy was - and even so, she may have been lucky. Giles, who was at least somewhat more experienced even at that stage, wouldn't go near the spell himself.
- Suicide. Faced with the shock of suddenly realising what their activities over the past goodness-knows-how-many years look like through normal human eyes, the vampire might well just self-destruct, as both Angel and Spike tried to do at some point. Although a callous hunter might say that that at least achieves the object of taking them out of circulation. But it would still mean no "vampire with a soul" left to muddle up the prophecy.
- They might just be naturally mean, anyway. Restoring the vampire's soul only gets them back to thinking like a normal human, and some humans kill people. So it doesn't guarantee that they'll no longer be a threat.
Life as a vampire is much easier if you're prepared to kill people. Even Angel was tempted sometimes, for instance when Darla nearly got him to bite Joyce. Spike was actively trying to be more murderous at one point because Buffy told him to (she'd become obsessed with the idea that they weren't tough enough to defeat their enemy), and he partly enjoyed it because the fact is Spike loves beating things up. Angel and Spike stopped themselves in time because they both seem to have started out as normal, decent people - decent enough to draw the line at murder, anyway. If it happened that the vampire had got ahead as a vampire because they were already a ruthless scumbag when they were human, they might look at their options and decide to just carry on as planned.
If everything did work out, then, although Buffy and the gang didn't know about this at the time of Series 2, there might be a fourth problem.
- Retribution. As seen in both Series 3 and Series 7, there is a powerful spirit being known as "the First Evil" that seems to really hate vampires changing sides, and will go to some effort to get the vampire either back or dead. The show has only shown it targeting the vampires themselves, but if somebody was making a habit of restoring vampires, then that person might be well advised to watch their back, too.
Perhaps (though I've no evidence in the series that that's the case) that's the real reason why there were no others like Angel. There were, briefly, but the First got them.