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My preference is for the pocket shorts. I currently own a 7mm with glued on pockets and a 5mm that I use with pocket shorts. My preference is for the shorts.
Glue on pockets:
-One issue with the glued on pockets is that you have to empty them in order to undress. The pockets will also reduce the amount of available stretch in the material of the leg, which makes dressing and undressing harder. I have an older Pinnacle semi-dry that is pretty stiff, which makes donning and doffing a bit of a fight anyway, and then the pockets just make it harder.
Pocket shorts:
-With the pocket shorts you can just pull the shorts off and throw them in the rinse bucket then hang them up to dry or throw them in your bag. All your stuff stays in the same place until you're at home and completely unpack.
-You can use the same ones on any suit you use.
Now, the pro of the glue on pockets. They look AWESOME! The pocket shorts, otherwise known as "geek shorts", are kinda geeky looking... Once you're suited up people will be in awe of the sheer awesomeness of your suit.
In the end, on my next suit I'll probably just leave it plain and use pocket shorts. I do love how the glue on pockets look, but the shorts are just so much more convenient for me that it's worth it.