long boring post follows....
This is always an issue. I see on other forums and ad spaces where people have bought multiple backpacks and cases in search of the right one, which some never find.
I suppose it depends on what you have and what your tasks are. I generally keep my most-used gear in a largish backpack, which includes camera, a few lenses, and the peripheral stuff like batteries and cards and whatnot. I try to keep everything I would vitally miss in there, so that I can always just pick up the pack and head off, knowing that even if I don't have everything optimal, I have something close. I don't use many filters but have the needed polarizers in the pack, Hoods fit with the lenses. Of course this possibility exists only if you do not have maximal sizes and amounts of stuff. My usual complement is a D7100 with 16-80 lens on it, an FX 70-300P, a 10-20 DXP, and a rotating couple of manual lenses depending on how I feel. I usually have my pet 35/2.8PC and an old 55/3.5, but those two spaces can take some other lens if I'm in the mood. I rarely carry a flash, but one could fit instead of a manual lens. The space is sufficient that I can mount some other lens on the camera and find a way, if tight, to stow the 16-80,though its big square hood must usually come off and go somewhere else. This all is pretty portable, though a bit heavy. Larger cameras and lenses could be less forgiving.
There's far more gear at home than I can carry, and I keep it all in a cabinet when not out in use. Lenses that don't fit into the backpack get taken separately when needed.
I've had some issues with fungus in the past, and advise not to store things at home inside their cases.
I used to carry an aluminum case with a foam liner which I custom tailored with razor knife, and found that if arranged just right this could work pretty well too. Most of the little accessories fit in the top behind a panel with various little pockets and loops. In the main body was room for the camera and several lenses, along with a flash and a couple of other things. Little spaces between things could hold film rolls, flash adapters and whatnot. The problem here is figuring out just what fits where best, and what size cutouts can be snug with a different mix of lenses. My F3 fit in this just right, but newer cameras and lenses did not, so it's out of service now. But this case had the advantage of being very secure and holding its contents better than one with the usual dividers. The dead space usually occupied by square corners and the dividers themselves can be cut out for small items, as long as the walls don't get too thin. It was worthwhile here to buy new foam from a craft store or the like rather than dividers or the stock foam that comes pre-cut in squares. The spaces can be a good fit to each component but still have enough flex to hold something else when needed without crumbling.
When flying, I take just the camera and the three lenses (normal zoom, tele, and wide), in a smaller pack with room for other small travel stuff (and of course cards and batteries and cloth and charger, etc.) Hoods are a bit of an issue, but can be stuffed in.
Otherwise I can't really contribute much, except to suggest that the little things you often forget should live in some central carrying case so you will always have them, even if the camera and lenses are taken loose. Get in the habit of putting them back in the case rather than on the shelf or table, and remember to take the case.