Automatically replacing depleted isotpe cells in breeders

Well, usually this involve filling up empty reactor spaces with either heat plating or other plating, and use a RP2 filter set to pull out re-enriched isotope cells and another RP2 filter set to pull out depleted isotope cell from a chest to the reactor. Eventually the breeding uranium cells will run out and the reactor will be full of depleted cells, and you need to manually restart it. It depends on the reactor design

grab yourself Logistic pipes and set them to extract cells
add a hopper on the reactor and set LP to supply hopper with depleted cells
got yourself a cool reactor

Though it wasn't in your list, if you have Railcraft, its loaders and unloaders make for wonderful automated breeder maintenance, especially with Buildcraft autocrafting tables.

Essentially, you have a Loader next to two autocrafting tables (one with the Depleted Isotope Cell recipe, the other with the Re-enriched -> Uranium cell recipe), set to Stock (not the default Transfer) at least one reactor load of components. It should load a unmoving (trapped/pinned by blocks, on a plain vanilla track) chest minecart, sitting on an Unloader adjacent to the reactor. The Unloader should be set to Stock the reactor with the appropriate number of components (e.g. 1 uranium cell, 4 depleted isotope cells).

Then you need a second loader/unloader pair, this time with the Loader adjacent to the reactor, set to Stock the cart with (some high number of) Re-Enriched Uranium Cells and Near-Depleted Uranium Cells. The Unloader doesn't need much for settings, just give it something to output to and manage the items as desired.

( =Loader, =Unloader, = Chest Minecart, = Reactor, = Autocrafting table, = irrelevant/spacer)

This has worked very, very reliably for me. It's even worked with a non-full reactor so far (ie filling it enough so there's no empty spaces before the uranium/isotopes, but leaving spaces after them), though maybe I've just gotten lucky with Minecraft's favored directions or somesuch.

Turns Breeders from a annoying maintenance task into a auto-magic resource generator :). The one hazard I've found is that if you connect the uranium-inserting loader/unloader pair on the side, as I have in that diagram, the Autocrafting tables are close enough to the reactor to be ignited if you're running it hot enough :p If you connect it to the top instead, that puts them out of danger (reactor top + 3 spaces, so only 9x9-size hazards would hit them directly))

Quote from Sliderpro

grab yourself Logistic pipes and set them to extract cells
add a hopper on the reactor and set LP to supply hopper with depleted cells
got yourself a cool reactor

Logipipes aren't that great as compared to RP2 Managers... and the version out now is actually a third-party release.

I actually recon LP crap all over RP2's pipe system, just like RP2's system they dont leak, move items around faster and have much more fine control over where items are going and coming from.

A retrievulator mode for manager would be nice, however this is not a place for RP2 suggestion..

Wasn't there a GregTech item which could place items in the reactor slot you wanted? I recall Greg mentioning that and I never could remember which block it was.

This is the setup I came up with to automate the process. A manager makes it a bit expensive as you need to keep both a damaged and undamaged version of each component you want to be in the reactor as it sees the two differently. The manager will pull depleted uranium and re-enriched isotope cells. These will then pass through item detectors. When the item detectors see either cell they will activate a corresponding filter to replace the missing item in the reactor.

Screenshot

(I tried to attach it but I obviously cannot do it correctly)

maybe a bit late but here is how i solved that problem

i set a RP2 sorting machine to automatic cycle to extract the re-enriched cells (no unnecessary lag by timer ticks). they passed an item detector which activated a state cell. this turned the breeder off for a short time (economical use of my uranium cell) and activated a timer to craft new isotope cells. that way i can keep my depleted cells in a stackable form and craft them into non-stackable isotope cells on demand.

if course you can redesign it without on demand management and just spam isotope cells (RP2 tubes are perfect for spamming inputs) but i think the main solution for the original problem would be to use a sorting machine in automatic cycle mode to extract the re-enriched cells.

Also late to the party but I'd like to share my solution to this as well - just IC2+BC.
http://i.imgur.com/U6jhGM5.png
On the right side there are chests for depleted cells and coal dust - we like to keep a huge supply of them.
Next is the buffer chest so we don't have to worry about overflows spilling.
Reactor chamber has an emerald pipe connected to it configured to pull out recharged cells and store them away.
When there's any vacant space inside the reactor the gates kick in and temporarily turn off the reactor to get maximum efficiency.
Reactor also gets turned off when the buffer chest is empty and is waiting for new isotope cells to be made.

It could probably be made fully automatic but as we have a double-chest full of recharged cell stacks there's not much need.
BC emerald pipes are a godsend.