I have the same problems that Diana outlined... don't want things in outer pockets, can't find phone with ease, etc.
My bags do have phone pockets, usually, but like Claire, I like the softer shapes which 'relax' and slip the phone out like a banana from a peel! Plus, I prefer a chunkier phone and some pockets are too small for it. Honestly, I've taken to looking for clothes with pockets big enough for my phone instead :-/ If I'm expecting calls, I actually remove the phone from the bag---though then I must remember where I put it down and not walk off without it!
I also rummage for pens and keys a LOT. I've tried using a rigid pencil case---easier to find, but they sound like a rattle when I walk around! This key loop thing sounds nifty. Maybe I should sew a few into my bags, at least those that are fabric-lined. Would be something like a bra-strap carrier, yes?
Make-up and meds and loose change have their own little pouches though---I think I got that idea from Jewell showing us her bag organization system in one of her older threads. Though I should remember to transfer loose change from wallet to pouch more regularly...
I've been eyeing purse organizers too. But I worry they wouldn't actually fit an assortment of bag shapes. Most seem to have a rectangular base, for instance, and at least a couple of by bags have a conical (basket-shaped) bottom or a deeply curved one...