Well, BC and RP2 systems aren't exclusive, there is no reason to restrict yourself to only using one. Overflow in both systems can be bad, Buildcraft is IMO better in this case because you can easily see where your system is broken, entities on the ground aren't big problem now, because they stack and you can reduce lifespan of items dropped by BC pipes. RP2 won't usually cause overflow, but when you manage to make infinite pipe storage, things can go really bad trying to fix it.
Here is a couple of overflow prevention systems that I use in my bee room:
It is catching additional drones going from my bee system to feed them to genepool (6 stacks of analyzed drones produces quite a good amount of BNA), if they won't fit in "any bee" part of pipe, they will go to "any", e.g. void pipe.
Another simple solution, use more machines. Random distribution of items in BC pipes is your friend here, items will overflow only if machines are almost full.
It is slightly more complicated system for squeezing honey. Iron pipe above the hopper has "inventory full" -> redstone signal, which reroutes items back to main line when hopper is full. There is a block behind iron pipe with redstone on top of it, which allows for correct loading of iron pipe redstone state while loading the game.
Here is scented paneling setup. Diamond pipes are routing wax, propolis and jellies to separate parts of the buffer. If any of the parts is full, that item will go further to storage. Planks are fed by autarchic gate next to ACT, which activates on "inventory empty". Emerald pipe only sends items, if carpenter have liquid and don't have work already. After this everything goes to AE bee product storage (I have second one only for serums, to search for them easier).