SnowleopardVK, our situations certainly are a bit different.
My problem is usually the reverse of yours--for Pathfinder/D&D, I typically have parties of six to eight players (sometimes more). In bigger parties, the GM's main challenge is in actually challenging the party with an encounter that's still balanced. In smaller groups... It can be a challenge to make an encounter that's meaningful and threatening without being a potential TPK.
Keep in mind that the APL in a small party is reduced by 1 if it's three players. Furthermore, your GM should certainly take the party's capabilities into account when designing encounters (undead are more of a threat without a cleric, rogues have to work harder to get flanking with fewer allies to flank with, and so forth).
One design philosophy that I've stuck to (and surprised that it's not more popular) is in mixing up encounter composition. For example, a dire lion (CR 5) is a reasonable challenge for a party with an APL of 5. So is a band of twelve orc warriors (at CR 1/3). In such a situation, the orcs have the advantage of numbers, but even a small party can take them on if they use smart tactics like bottle-necking them. Furthermore, the characters get to have a "moment of awesome" because they so easily outclass the low-CR critters. They'll hit more often and get hit less often, and it's pretty cool to get that sense of scale as you level up.
As for your particular situation... If there are only three players and you're determined to have a game, I'd probably allow the players to run two characters each. Not only would it make the party more survivable and versatile, but players don't feel like they're getting hosed with a character they don't like.