At the Experience event this weekend, I got the chance to try both models extensively. I spent two hours playing them and comparing them.
I agree with what most people are saying about them and their tone - the Custom is more "dark" overall, with lower lows and highs that are perhaps less shrill, while the Standard seems to have strong mids.
That being said, I found that for me the Standard was much more versatile tonally. I play lots of different styles on an acoustic, and use it in solo situations as well as for accompanying vocals or other instruments, and additionally for layering guitar sounds in a recording situation.
While playing them on Friday I did some rock and country strumming, played some Tommy Emmanuel, Steve Howe, and Tony McManus fingerstyle covers, tried some Delta blues, open tuned it, capo-ed it, slapped and tapped some Andy McKee tunes and Rodrigo y Gabriela covers. I played some bossa-nova and some bluegrass. I tried everything that I could think of on the thing to see how they would each respond to different playing situations. For my ears, the Standard model performed best across the spectrum of playing styles that I would be applying it to. It gave me everything I needed, tone-wise, for all these different approaches. I never felt it was lacking in the low end, even for the Celtic stuff tuned way down (I went to low C for Jimmy Page's Bron Yr Aur). It took the capo really well, and sounded particularly "chimey" with the capo above the 5th fret. The tone of the Standard is very balanced.
After spending the entire afternoon playing these things - switching between the two frequently and taking them both through the paces - I bought the Standard.
For me, the decision wasn't even about tone. It was about aesthetics. I didn't care for the way the white plastic binding contrasted against the dark wood of the Custom model. It was just too stark a contrast and seemed to look a bit cheaper. It was must less a contrast against the mahogany of the Standard model, and I felt that the instrument kept the appearance of higher quality that way.
In the end, it will come down to your personal preference, but I have to say that you cannot go wrong no matter which model you choose. The SE Angelus is a wonderful guitar to own. I have hardly put mine down since I bought it.
Good luck with your choice!
-Dale