Strange you mention both Guess Man and Issey! Small small world...because I own both of those and I had a similar experience...
I wore Issey Miyake to school the other day and asked my g/f what she thought it was. She said "Guess Man". I said "no..." she said "oh then it's issey miyake"
I can DEFINATELY smell the difference..even after the dry down... I don't get how people can confuse them!
First of all...top notes are different. Issey is floral/odd smell (probably that Japanese Yuzu stuff) and Guess smells like sweet fresh masculine apples.
The dry downs... Issey is woody/citrusy slightly with florals. Guess Man is sweet green smelling with some woods and citrus...no florals to me.
Smell again! put one of each wrist. they smell different but may share a common woody/citrus note?
They both get excellent longevity on me. The best two in my wardrobe with Platinum Egoiste not too far behind. Sillage for Issey is more at first, but when they dry down, sillage is about equal.