Yes, it is more fun...
But yeah I see your point. so what would you suggest that would make sense? Would have to be something other than money. More street cred?
Yes, I have always believed that there should be some reward or punishment when it comes to following mission parameters.
I honestly believe that you should either receive more street cred and / or eddies for doing things Regina's way, or there should be some mechanism for Regina to simply not give you any more work if you don't do as she asks.
There is a conversation between two mercs in the Afterlife where one merch chastises the other for trying to double-cross Regina and she ends up completely cutting off jobs for him. If you just run around capping Cyberpsychos rather than take them alive like Regina requested, the Cyberpsycho quest line should just dry up. If V cannot do the job properly, Regina should just go find some mercs who can.
I am not sure if a faction system needs to be in place, but something additional is definitely needed in order to add difficulty and also introduce incentives and negative consequences to your actions.
There should also be an avenue to repairing your rep should you want to get back in the good graces of the fixer you just annoyed.
It would also be nice if the Cyberpsycho quest line had a satisfying plot ending like Regina telling you that the data gathered will go towards researching the condition and maybe finding treatments. Right now, the quest just ends with "Thanks, V!" and some loot.