I grew up, literally, on Oly's Super Control Panel and customizability of their cameras' control from the days of the C7070. And I loved it. I don't get the Nikons nor Canons. And I was using a Canon before moving to Oly. And I had the pleasure of the D300 for a while. I used the G1 for a while, too. And didn't like it. BTW a while for myself means at least a month, if not more, of using the camera; not just pushing buttons at the counter of some camera shop.
Both the EP3 and GX1 are highly customisable cameras. You can literally set them to function exactly as how you would like the controls to be. And the GX1 takes it a step further. In the EP3, "MySet" are in the Menu Options. With the GX1, it is in the Mode dial. Just like in the C7070 (Olympus should really re-look the design of the C7070 - that is still one of the most ergonomically designed digital camera I have used). Turn the Mode dial and you are there - no menu hunting.
The buttons in the GX1 are more logical. AE/AF Lock in the GX1 is where it makes sense, like all Oly's cameras prior to the EP3 (the E-series dSLRs, EP1/2), at where the thumb can reach. In the EP3, Oly took it out (of course you can put it where you want but the fact remains that Oly did NOT label a button AE/AF Lock ...) and replaced it with a "Movie" button by default (you can still change it back to AE/AF Lock). And I like it that the GX1 has a dedicated AF mode button. The GX1 doesn't allow you to customise the 4 selector buttons unlike the EP3 which allows you to customise 2 of the selectors. The EP3's trump button here is the "Trash" button. Who doesn't want a quick way to delete pics? It is definitely more tedious to delete pics in the GX1. The "Movie" Fn button in the GX1 definitely makes a lot of sense. It is the only way to get into Movie mode. With one step overriding whatever you set in on the Mode Dial. With the EP3, there is actually a Movie Mode in the Selector Dial, which do make the Movie Button a little redundant. I also like the GX1's one button mode to IA (Panny's Super-Everything-Auto Mode); when in doubt or u need one button access for THAT split second moment, reach for this button. On the EP3, it also exist in the Selector Dial as iAuto. Again, debatable which is a more ergonomic way to do things, though I do like the "Movie" button in the GX1 and its position. I don't like the position of the "Movie" button in the EP3. There are also some not very apparent limitations to the functions you can assign to the various EP3's button.
As a test, try to set the Exposure Compensation +/- on either one. Then use it.
As for customising via the LCD screen, the GX1 definitely has the upper hand here. Practically every function is touch related on the LCD screen in the GX1 versus using the "wheel up/down or left/right" on the EP3. I really don't like the "wheel" in the EP1/2/3. I much prefer the 4 buttons selectors as in the Oly's dSLRS. The "wheel" is NOT reassuring, and if I had like that, I would have stayed on with Canon .....just saying
There are many occasions when this "loose" wheel actually changed my settings without my knowledge. I love Oly's SCP but they really lost me with the "Live Control". It is not fully apparent to myself even now how I control this "Live Control" ..... With the GX1, it is certainly more intuitive - use your finger on the LCD screen itself if in doubt.
I really like the "Q.Menu" button bringing up a "Quick" menu that is brilliant in its implementation in the GX1. If you guys use Firefox, you'll understand what I mean. Drag and drop on the LCD screen itself. Literally any function. And then access that function in 2 steps.
The EP3 however allows for MORE option in the ability to customise. It even allows for direction of dial and controls (e.g. F-Stops, shutter speeds). What I miss in the GX1 is the ability of the EP3 to define the size of the files and more levels of compression. In the GX1, the file size for jpgs is fixed at either L, M or S and quality of compression is either "Good" or "Std", with or without RAW. For jpgs in the EP3, you can decide the resolutions of L, M and S and the level of compression is SF, F or N.
In summary, I think the EP3 allows for MORE customisation but the GX1 does it in a more logical manner. Both are very flexible and can probably accommodate most photographers who knows what they want.