As a current owner of both watches, I can only give you feedback based on your two choices. At the end of the day, which watch you choose is entirely up to you.
The Aquanaut has the advantage of being a Patek (brand name like you mentioned). Mine came on a metal bracelet so I do not have first hand experience of the rubber strap. One thing that I must highlight to you is that the caliber 324SC in the Aquanaut does not hack. Some may find this annoying but honestly, this does not affect the accuracy of the watch as a daily wearer. The Aquanaut is a watch that you can dress up or down and with a 120m WR, is very versatile as a sports watch. I would think the disadvantage you mention for the Aquanaut is similiar to a person feeling that he bought a submariner because he could not afford a seadweller. I would say that it is a little unfounded as both are different in design.
The 15400ST is, as you mentioned, a design of Genta's so it is iconic. Movement hacks and handwind and is accurate. One thing i would like to highlight is that the bracelet of the 15400ST tugs at the hairs on my arm but this may not bother you. At 41mm, it does wear bigger. If you are a fan of simplicity, then the AP is the way to go as the dial is less busy as compared to the Aquanaut.