I have not had to pay custom in any of my package from JP.
I would base ems/fedex purely on $. From experience tho, Fedex really do rush the package through custom but with EMS and I think I've had EMS held a day or 2 longer.
If you are ordering stuff with litium battery, it is best to go with Fedex. with Gunpla/figure/non electronics, I really don't feel it matter much and would chose base on quoted price.
for fun, some random tracking info from my previous orders. fedex tracking vs ems. (do note that they ship from different location in JP and not from HLJ tho I ordered a few time from them )
edit: blah formatting is all mess up, too lazy to use screenshot. first part is fedex, 2nd is ems
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01/07/2013 - Monday
09:59
Delivered
LOS ANGELES, CA
07:09
On FedEx vehicle for delivery
LOS ANGELES, CA
07:05
At local FedEx facility
LOS ANGELES, CA
04:40
In transit
LOS ANGELES, CA
-
30/06/2013 - Sunday
14:51
Departed FedEx location
MEMPHIS, TN
10:34
International shipment release - Import
MEMPHIS, TN
03:15
Arrived at FedEx location
MEMPHIS, TN
05:01
In transit
SENNAN-SHI JP
00:28
In transit
SENNAN-SHI JP
-
29/06/2013 - Saturday
14:48
Left FedEx origin facility
KADOMA-SHI JP
09:51
Picked up
KADOMA-SHI JP
-
28/06/2013 - Friday
03:58
Shipment information sent to FedEx
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EMS
Delivered
April 4, 2013, 10:45 am
Out for Delivery
April 4, 2013, 8:37 am
LOS ANGELES, CA 90027
Sorting Complete
April 4, 2013, 8:27 am
LOS ANGELES, CA 90027
Arrival at Post Office
April 4, 2013, 8:13 am
LOS ANGELES, CA 90027
Inbound Out of Customs
April 4, 2013, 3:24 am
Processed through USPS Sort Facility
April 4, 2013, 2:29 am
LOS ANGELES, CA 90009
Inbound Into Customs
Processed Through Sort Facility
April 2, 2013, 6:49 pm
ISC LOS ANGELES CA (USPS)
Origin Post is Preparing Shipment
Processed Through Sort Facility
April 2, 2013, 11:40 am
TOKYO INT CONTAINER 1, JAPAN
Processed Through Sort Facility
April 1, 2013, 11:04 pm
TOKYO INT CONTAINER 1, JAPAN
Acceptance
April 1, 2013, 6:45 pm
JAPAN