Here's why you'd want more advanced species:
1) More advanced species often produce their given comb faster
2) More advanced species are almost always needed as stepping stones to very, very good bees (for example, you would want to breed a bunch of Resilient bees to get bees like Valuable, Glittering, Radioactive, Impregnable, Invincible, etc)
3) More advanced species often have better products (for example, Demonic > Fiendish > Sinister; all three produce Simmering Combs, but Demonic produces Glowstone Dust as a side product and Fiendish produces Ash as a side product)
4) More advanced species sometimes have less negative effects or sometimes even positive ones (for example, Demonic > Fiendish > Sinister; Fiendish and Sinister have Aggress, which does 4 hearts of damage per second and really needs an Apiarist's Suit to deal with, but Demonic only sets you on fire, which is easily cured with water; also Edenic > Exotic > Tropical; Edenic gives you experience, Exotic has no effect (?) and Tropical poisons you for ~40 seconds)
Here's why you wouldn't:
1) The traits almost always don't change from species to species IF they are in the same branch and stay mostly the same; major exceptions are the Farmed branch, the various colors, the Skulking/Vis/Thaumic branches from Thaumic Bees; note that traits often change when the branch changes; exception to this rule is all of the mineral bees, where the traits are almost all the same from species to species
If you have purebred species that you want to auto-farm, you could use a plain Diamond Pipe instead of an Apiarist's Pipe, although this still presents a problem of cost. I'm not sure of the exact machine, but I'm almost certain that if you look through RedPower, you could find a machine that could do the job automatically for you. Pneumatic Tubes are a little more expensive and less intuitive, but they're worth it overall.